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UniProtKB - P60340 (TRUB_ECOLI)

Entry version 143 (07 Apr 2021)
Sequence version 1 (16 Feb 2004)
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Protein

tRNA pseudouridine synthase B

Gene

truB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs.UniRule annotation2 Publications

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

  1. KM=148 nM for tRNA (at pH 7.5)1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei43SubstrateUniRule annotation1 Publication1
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei48NucleophileUniRule annotation1 Publication1
    Binding sitei76SubstrateUniRule annotation1 Publication1
    Binding sitei179SubstrateUniRule annotation1 Publication1
    Binding sitei202SubstrateUniRule annotation1 Publication1

    <p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

    Complete GO annotation on QuickGO ...

    GO - Biological processi

    Complete GO annotation on QuickGO ...

    <p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

    Molecular functionIsomerase
    Biological processtRNA processing

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...    BioCyci    		EcoCyc:EG11177-MONOMER
    MetaCyc:EG11177-MONOMER

    BRENDA Comprehensive Enzyme Information System

    More...    BRENDAi    		5.4.99.25, 2026

    <p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
    Recommended name:
    tRNA pseudouridine synthase BUniRule annotation (EC:5.4.99.25UniRule annotation1 Publication)
    Alternative name(s):
    Protein P351 Publication
    tRNA pseudouridine(55) synthaseUniRule annotation
    Short name:
    Psi55 synthaseUniRule annotation
    tRNA pseudouridylate synthaseUniRule annotation
    tRNA-uridine isomeraseUniRule annotation
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
    Name:truB
    Synonyms:yhbA
    Ordered Locus Names:b3166, JW3135
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
    • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    <p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

    <p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi19K → M or R: Reduced structural stability and decrease in activity. 1 Publication1
    Mutagenesisi20P → G or L: Reduced structural stability and no change in activity. 1 Publication1
    Mutagenesisi43H → A: 330-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi43H → F: 2-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi43H → G: 250-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi43H → N: 180-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi43H → Q: 50-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi48D → C: Loss of activity. 1 Publication1
    Mutagenesisi58C → A: Slight increase in activity. Slight increase in activity; when associated with A-174 and A-193. 1 Publication1
    Mutagenesisi174C → A: Slight increase in activity. Slight increase in activity; when associated with A-58 and A-193. 1 Publication1
    Mutagenesisi193C → A: Slight increase in activity; when associated with A-58 and A-174. 1 Publication1
    Mutagenesisi193C → V: Slight increase in activity. 1 Publication1

    <p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001218301 – 314tRNA pseudouridine synthase BAdd BLAST314

    Proteomic databases

    jPOST - Japan Proteome Standard Repository/Database

    More...    jPOSTi    		P60340

    PaxDb, a database of protein abundance averages across all three domains of life

    More...    PaxDbi    		P60340

    PRoteomics IDEntifications database

    More...    PRIDEi    		P60340

    <p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

    <p>This subsection of the 'Expression' section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

    Weakly expressed in maxicells, part of the metY operon that extends to pnp (PubMed:2849753).1 Publication

    <p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

    Protein-protein interaction databases

    Protein interaction database and analysis system

    More...    IntActi    		P60340, 5 interactors

    STRING: functional protein association networks

    More...    STRINGi    		511145.b3166

    <p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

    Secondary structure

    1314
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    SWISS-MODEL Repository - a database of annotated 3D protein structure models

    More...    SMRi    		P60340

    Database of comparative protein structure models

    More...    ModBasei    		Search...

    Protein Data Bank in Europe - Knowledge Base

    More...    PDBe-KBi    		Search...

    Miscellaneous databases

    Relative evolutionary importance of amino acids within a protein sequence

    More...    EvolutionaryTracei    		P60340

    <p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni124 – 152RNA bindingBy similarityAdd BLAST29

    <p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

    Belongs to the pseudouridine synthase TruB family. Type 1 subfamily.UniRule annotationCurated

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...    eggNOGi    		COG0130, Bacteria

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...    HOGENOMi    		CLU_032087_0_3_6

    InParanoid: Eukaryotic Ortholog Groups

    More...    InParanoidi    		P60340

    Database for complete collections of gene phylogenies

    More...    PhylomeDBi    		P60340

    Family and domain databases

    Conserved Domains Database

    More...    CDDi    		cd02573, PseudoU_synth_EcTruB, 1 hit

    Gene3D Structural and Functional Annotation of Protein Families

    More...    Gene3Di    		2.30.130.10, 1 hit

    HAMAP database of protein families

    More...    HAMAPi    		MF_01080, TruB_bact, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...    InterProi    		View protein in InterPro
    IPR020103, PsdUridine_synth_cat_dom_sf
    IPR002501, PsdUridine_synth_N
    IPR015947, PUA-like_sf
    IPR036974, PUA_sf
    IPR014780, tRNA_psdUridine_synth_TruB
    IPR015240, tRNA_sdUridine_synth_fam1_C
    IPR032819, TruB_C

    The PANTHER Classification System

    More...    PANTHERi    		PTHR13767, PTHR13767, 1 hit

    Pfam protein domain database

    More...    Pfami    		View protein in Pfam
    PF09157, TruB-C_2, 1 hit
    PF16198, TruB_C_2, 1 hit
    PF01509, TruB_N, 1 hit

    Superfamily database of structural and functional annotation

    More...    SUPFAMi    		SSF55120, SSF55120, 1 hit
    SSF88697, SSF88697, 1 hit

    TIGRFAMs; a protein family database

    More...    TIGRFAMsi    		TIGR00431, TruB, 1 hit

    <p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

    P60340-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MSRPRRRGRD INGVLLLDKP QGMSSNDALQ KVKRIYNANR AGHTGALDPL 
            60         70         80         90        100
    ATGMLPICLG EATKFSQYLL DSDKRYRVIA RLGQRTDTSD ADGQIVEERP 
           110        120        130        140        150
    VTFSAEQLAA ALDTFRGDIE QIPSMYSALK YQGKKLYEYA RQGIEVPREA 
           160        170        180        190        200
    RPITVYELLF IRHEGNELEL EIHCSKGTYI RTIIDDLGEK LGCGAHVIYL 
           210        220        230        240        250
    RRLAVSKYPV ERMVTLEHLR ELVEQAEQQD IPAAELLDPL LMPMDSPASD 
           260        270        280        290        300
    YPVVNLPLTS SVYFKNGNPV RTSGAPLEGL VRVTEGENGK FIGMGEIDDE 
           310 
    GRVAPRRLVV EYPA
    Length:314
    Mass (Da):35,087
    Last modified:February 16, 2004 - v1
    <p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iFEA46C01E0E8E7A5
    GO

    Sequence databases

    Select the link destinations:

    EMBL nucleotide sequence database

    More...    EMBLi

    GenBank nucleotide sequence database

    More...    GenBanki

    DNA Data Bank of Japan; a nucleotide sequence database

    More...    DDBJi
    Links Updated
    		X13270 Genomic DNA Translation: CAA31635.1
    X13775 Genomic DNA Translation: CAA32021.1
    U18997 Genomic DNA Translation: AAA57969.1
    U00096 Genomic DNA Translation: AAC76200.1
    AP009048 Genomic DNA Translation: BAE77212.1
    S79856 Genomic DNA Translation: AAB35645.1

    Protein sequence database of the Protein Information Resource

    More...    PIRi    		S01916, Q9EC35

    NCBI Reference Sequences

    More...    RefSeqi    		NP_417635.1, NC_000913.3
    WP_000089698.1, NZ_STEB01000012.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...    EnsemblBacteriai    		AAC76200; AAC76200; b3166
    BAE77212; BAE77212; BAE77212

    Database of genes from NCBI RefSeq genomes

    More...    GeneIDi    		58348663
    947687

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...    KEGGi    		ecj:JW3135
    eco:b3166

    Pathosystems Resource Integration Center (PATRIC)

    More...    PATRICi    		fig|1411691.4.peg.3564

    <p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

    <p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    		X13270 Genomic DNA Translation: CAA31635.1
    X13775 Genomic DNA Translation: CAA32021.1
    U18997 Genomic DNA Translation: AAA57969.1
    U00096 Genomic DNA Translation: AAC76200.1
    AP009048 Genomic DNA Translation: BAE77212.1
    S79856 Genomic DNA Translation: AAB35645.1
    PIRiS01916, Q9EC35
    RefSeqiNP_417635.1, NC_000913.3
    WP_000089698.1, NZ_STEB01000012.1

    3D structure databases

    Select the link destinations:

    Protein Data Bank Europe

    More...    PDBei

    Protein Data Bank RCSB

    More...    RCSB PDBi

    Protein Data Bank Japan

    More...    PDBji
    Links Updated
    		PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1K8WX-ray1.85A7-314[»]
    1R3FX-ray1.85A1-314[»]
    1ZL3X-ray2.80A10-314[»]
    SMRiP60340
    ModBaseiSearch...
    PDBe-KBiSearch...

    Protein-protein interaction databases

    IntActiP60340, 5 interactors
    STRINGi511145.b3166

    Proteomic databases

    jPOSTiP60340
    PaxDbiP60340
    PRIDEiP60340

    Genome annotation databases

    EnsemblBacteriaiAAC76200; AAC76200; b3166
    BAE77212; BAE77212; BAE77212
    GeneIDi58348663
    947687
    KEGGiecj:JW3135
    eco:b3166
    PATRICifig|1411691.4.peg.3564

    Organism-specific databases

    EchoBASE - an integrated post-genomic database for E. coli

    More...    EchoBASEi    		EB1164

    Phylogenomic databases

    eggNOGiCOG0130, Bacteria
    HOGENOMiCLU_032087_0_3_6
    InParanoidiP60340
    PhylomeDBiP60340

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11177-MONOMER
    MetaCyc:EG11177-MONOMER
    BRENDAi5.4.99.25, 2026

    Miscellaneous databases

    EvolutionaryTraceiP60340

    Protein Ontology

    More...    PROi    		PR:P60340

    Family and domain databases

    CDDicd02573, PseudoU_synth_EcTruB, 1 hit
    Gene3Di2.30.130.10, 1 hit
    HAMAPiMF_01080, TruB_bact, 1 hit
    InterProiView protein in InterPro
    IPR020103, PsdUridine_synth_cat_dom_sf
    IPR002501, PsdUridine_synth_N
    IPR015947, PUA-like_sf
    IPR036974, PUA_sf
    IPR014780, tRNA_psdUridine_synth_TruB
    IPR015240, tRNA_sdUridine_synth_fam1_C
    IPR032819, TruB_C
    PANTHERiPTHR13767, PTHR13767, 1 hit
    PfamiView protein in Pfam
    PF09157, TruB-C_2, 1 hit
    PF16198, TruB_C_2, 1 hit
    PF01509, TruB_N, 1 hit
    SUPFAMiSSF55120, SSF55120, 1 hit
    SSF88697, SSF88697, 1 hit
    TIGRFAMsiTIGR00431, TruB, 1 hit

    ProtoNet; Automatic hierarchical classification of proteins

    More...    ProtoNeti    		Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...    MobiDBi    		Search...

    <p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

    <p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiTRUB_ECOLI
    <p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P60340
    Secondary accession number(s): P09171, P76671, Q2M944
    <p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 16, 2004
    Last sequence update: February 16, 2004
    Last modified: April 7, 2021
    This is version 143 of the entry and version 1 of the sequence. See complete history.
    <p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    <p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
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