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Q9GZU7

- CTDS1_HUMAN

UniProt

Q9GZU7 - CTDS1_HUMAN

Protein

Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1

Gene

CTDSP1

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 119 (01 Oct 2014)
      Sequence version 1 (01 Mar 2001)
      Previous versions | rss
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    Functioni

    Preferentially catalyzes the dephosphorylation of 'Ser-5' within the tandem 7 residue repeats in the C-terminal domain (CTD) of the largest RNA polymerase II subunit POLR2A. Negatively regulates RNA polymerase II transcription, possibly by controlling the transition from initiation/capping to processive transcript elongation. Recruited by REST to neuronal genes that contain RE-1 elements, leading to neuronal gene silencing in non-neuronal cells.2 Publications

    Catalytic activityi

    [a protein]-serine/threonine phosphate + H2O = [a protein]-serine/threonine + phosphate.

    Cofactori

    Binds 1 magnesium ion per monomer.

    Enzyme regulationi

    Stimulated by GTF2F1. Inhibited by beryllofluoride anions.1 Publication

    pH dependencei

    Optimum pH is 5.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei96 – 9614-aspartylphosphate intermediate
    Metal bindingi96 – 961Magnesium1 Publication
    Active sitei98 – 981Proton donor
    Metal bindingi98 – 981Magnesium; via carbonyl oxygen1 Publication
    Sitei152 – 1521Transition state stabilizer
    Sitei190 – 1901Transition state stabilizer
    Metal bindingi207 – 2071Magnesium1 Publication

    GO - Molecular functioni

    1. CTD phosphatase activity Source: UniProtKB
    2. metal ion binding Source: UniProtKB-KW
    3. protein binding Source: UniProtKB

    GO - Biological processi

    1. negative regulation of neurogenesis Source: Ensembl
    2. negative regulation of neuron differentiation Source: Ensembl
    3. protein dephosphorylation Source: UniProtKB
    4. regulation of transcription from RNA polymerase II promoter Source: UniProtKB

    Keywords - Molecular functioni

    Hydrolase, Protein phosphatase

    Keywords - Ligandi

    Metal-binding

    Enzyme and pathway databases

    SignaLinkiQ9GZU7.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 (EC:3.1.3.16)
    Alternative name(s):
    Nuclear LIM interactor-interacting factor 3
    Short name:
    NLI-IF
    Short name:
    NLI-interacting factor 3
    Small C-terminal domain phosphatase 1
    Short name:
    SCP1
    Short name:
    Small CTD phosphatase 1
    Gene namesi
    Name:CTDSP1
    Synonyms:NIF3, NLIIF, SCP1
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 2

    Organism-specific databases

    HGNCiHGNC:21614. CTDSP1.

    Subcellular locationi

    Nucleus 1 Publication
    Note: Colocalizes with RNA polymerase II.

    GO - Cellular componenti

    1. extracellular vesicular exosome Source: UniProt
    2. nucleus Source: UniProtKB

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi96 – 961D → E: No effect. Completely abolishes phosphatase activity; when associated with N-98. 1 Publication
    Mutagenesisi98 – 981D → N: Completely abolishes phosphatase activity; when associated with E-96. 1 Publication

    Organism-specific databases

    PharmGKBiPA134938848.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 261261Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1PRO_0000212572Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei1 – 11N-acetylmethionine1 Publication

    Keywords - PTMi

    Acetylation

    Proteomic databases

    MaxQBiQ9GZU7.
    PaxDbiQ9GZU7.
    PRIDEiQ9GZU7.

    PTM databases

    PhosphoSiteiQ9GZU7.

    Expressioni

    Tissue specificityi

    Expression is restricted to non-neuronal tissues. Highest expression in skeletal muscle, spleen, lung and placenta.1 Publication

    Gene expression databases

    BgeeiQ9GZU7.
    CleanExiHS_CTDSP1.
    GenevestigatoriQ9GZU7.

    Interactioni

    Subunit structurei

    Monomer By similarity. Interacts with GTF2F1. Interacts with REST.By similarity4 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    Ctdsp1P584662EBI-751587,EBI-7091612From a different organism.

    Protein-protein interaction databases

    BioGridi121804. 5 interactions.
    IntActiQ9GZU7. 2 interactions.
    MINTiMINT-1441843.
    STRINGi9606.ENSP00000273062.

    Structurei

    Secondary structure

    1
    261
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi85 – 873
    Beta strandi92 – 954
    Turni99 – 1013
    Beta strandi102 – 1076
    Beta strandi113 – 1208
    Beta strandi123 – 1319
    Helixi135 – 14511
    Beta strandi146 – 1516
    Helixi156 – 16611
    Beta strandi172 – 1765
    Helixi178 – 1803
    Beta strandi181 – 1844
    Beta strandi187 – 1893
    Helixi192 – 1943
    Beta strandi195 – 1973
    Helixi199 – 2013
    Beta strandi202 – 2054
    Helixi209 – 2124
    Helixi216 – 2183
    Beta strandi219 – 2213
    Helixi233 – 24412
    Helixi251 – 2544

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1T9ZX-ray2.30A77-261[»]
    1TA0X-ray2.10A77-261[»]
    2GHQX-ray2.05A/B77-256[»]
    2GHTX-ray1.80A/B77-256[»]
    3L0BX-ray2.35A/B77-256[»]
    3L0CX-ray2.45A/B77-256[»]
    3L0YX-ray2.30A/B77-256[»]
    3PGLX-ray2.35A/B77-256[»]
    ProteinModelPortaliQ9GZU7.
    SMRiQ9GZU7. Positions 77-256.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9GZU7.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini86 – 244159FCP1 homologyPROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Contains 1 FCP1 homology domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG5190.
    HOGENOMiHOG000236379.
    HOVERGENiHBG053298.
    InParanoidiQ9GZU7.
    KOiK15731.
    OrthoDBiEOG71P2C3.
    PhylomeDBiQ9GZU7.
    TreeFamiTF313556.

    Family and domain databases

    Gene3Di3.40.50.1000. 1 hit.
    InterProiIPR011948. Dullard_phosphatase.
    IPR023214. HAD-like_dom.
    IPR004274. NIF.
    [Graphical view]
    PfamiPF03031. NIF. 1 hit.
    [Graphical view]
    SMARTiSM00577. CPDc. 1 hit.
    [Graphical view]
    SUPFAMiSSF56784. SSF56784. 1 hit.
    TIGRFAMsiTIGR02251. HIF-SF_euk. 1 hit.
    PROSITEiPS50969. FCP1. 1 hit.
    [Graphical view]

    Sequences (3)i

    Sequence statusi: Complete.

    This entry describes 3 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q9GZU7-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MDSSAVITQI SKEEARGPLR GKGDQKSAAS QKPRSRGILH SLFCCVCRDD    50
    GEALPAHSGA PLLVEENGAI PKQTPVQYLL PEAKAQDSDK ICVVIDLDET 100
    LVHSSFKPVN NADFIIPVEI DGVVHQVYVL KRPHVDEFLQ RMGELFECVL 150
    FTASLAKYAD PVADLLDKWG AFRARLFRES CVFHRGNYVK DLSRLGRDLR 200
    RVLILDNSPA SYVFHPDNAV PVASWFDNMS DTELHDLLPF FEQLSRVDDV 250
    YSVLRQPRPG S 261
    Length:261
    Mass (Da):29,203
    Last modified:March 1, 2001 - v1
    Checksum:i75A430BCA2748FEA
    GO
    Isoform 2 (identifier: Q9GZU7-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         73-73: Missing.

    Show »
    Length:260
    Mass (Da):29,075
    Checksum:i30B0CCD745F26DBB
    GO
    Isoform 3 (identifier: Q9GZU7-3) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-22: MDSSAVITQISKEEARGPLRGK → MVAAPWATQEQEEGRGIQPGDR
         73-73: Missing.

    Note: No experimental confirmation available.

    Show »
    Length:260
    Mass (Da):29,128
    Checksum:iD7741284DEE4D3B5
    GO

    Sequence cautioni

    The sequence AAP34398.1 differs from that shown. Reason: Frameshift at position 72.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti180 – 1801S → F in BX446444. 1 PublicationCurated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti56 – 561A → T.
    Corresponds to variant rs2227249 [ dbSNP | Ensembl ].
    VAR_049054

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 2222MDSSA…PLRGK → MVAAPWATQEQEEGRGIQPG DR in isoform 3. 1 PublicationVSP_045865Add
    BLAST
    Alternative sequencei73 – 731Missing in isoform 2 and isoform 3. 2 PublicationsVSP_045866

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF229163 Genomic DNA. Translation: AAG15404.1.
    AF229162 mRNA. Translation: AAG15402.1.
    AY279529 mRNA. Translation: AAP34397.1.
    AY279530 mRNA. Translation: AAP34398.1. Frameshift.
    BX446444 mRNA. No translation available.
    AC021016 Genomic DNA. No translation available.
    BC012977 mRNA. Translation: AAH12977.1.
    CCDSiCCDS2416.1. [Q9GZU7-1]
    CCDS56166.1. [Q9GZU7-3]
    RefSeqiNP_001193807.1. NM_001206878.1. [Q9GZU7-3]
    NP_067021.1. NM_021198.2. [Q9GZU7-1]
    NP_872580.1. NM_182642.2. [Q9GZU7-2]
    UniGeneiHs.444468.

    Genome annotation databases

    EnsembliENST00000273062; ENSP00000273062; ENSG00000144579. [Q9GZU7-1]
    ENST00000443891; ENSP00000392248; ENSG00000144579. [Q9GZU7-3]
    GeneIDi58190.
    KEGGihsa:58190.
    UCSCiuc002vhy.3. human. [Q9GZU7-1]
    uc002vhz.3. human. [Q9GZU7-2]

    Polymorphism databases

    DMDMi17865510.

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF229163 Genomic DNA. Translation: AAG15404.1 .
    AF229162 mRNA. Translation: AAG15402.1 .
    AY279529 mRNA. Translation: AAP34397.1 .
    AY279530 mRNA. Translation: AAP34398.1 . Frameshift.
    BX446444 mRNA. No translation available.
    AC021016 Genomic DNA. No translation available.
    BC012977 mRNA. Translation: AAH12977.1 .
    CCDSi CCDS2416.1. [Q9GZU7-1 ]
    CCDS56166.1. [Q9GZU7-3 ]
    RefSeqi NP_001193807.1. NM_001206878.1. [Q9GZU7-3 ]
    NP_067021.1. NM_021198.2. [Q9GZU7-1 ]
    NP_872580.1. NM_182642.2. [Q9GZU7-2 ]
    UniGenei Hs.444468.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1T9Z X-ray 2.30 A 77-261 [» ]
    1TA0 X-ray 2.10 A 77-261 [» ]
    2GHQ X-ray 2.05 A/B 77-256 [» ]
    2GHT X-ray 1.80 A/B 77-256 [» ]
    3L0B X-ray 2.35 A/B 77-256 [» ]
    3L0C X-ray 2.45 A/B 77-256 [» ]
    3L0Y X-ray 2.30 A/B 77-256 [» ]
    3PGL X-ray 2.35 A/B 77-256 [» ]
    ProteinModelPortali Q9GZU7.
    SMRi Q9GZU7. Positions 77-256.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 121804. 5 interactions.
    IntActi Q9GZU7. 2 interactions.
    MINTi MINT-1441843.
    STRINGi 9606.ENSP00000273062.

    Chemistry

    BindingDBi Q9GZU7.
    ChEMBLi CHEMBL1795098.

    PTM databases

    PhosphoSitei Q9GZU7.

    Polymorphism databases

    DMDMi 17865510.

    Proteomic databases

    MaxQBi Q9GZU7.
    PaxDbi Q9GZU7.
    PRIDEi Q9GZU7.

    Protocols and materials databases

    DNASUi 58190.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000273062 ; ENSP00000273062 ; ENSG00000144579 . [Q9GZU7-1 ]
    ENST00000443891 ; ENSP00000392248 ; ENSG00000144579 . [Q9GZU7-3 ]
    GeneIDi 58190.
    KEGGi hsa:58190.
    UCSCi uc002vhy.3. human. [Q9GZU7-1 ]
    uc002vhz.3. human. [Q9GZU7-2 ]

    Organism-specific databases

    CTDi 58190.
    GeneCardsi GC02P219262.
    HGNCi HGNC:21614. CTDSP1.
    MIMi 605323. gene.
    neXtProti NX_Q9GZU7.
    PharmGKBi PA134938848.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG5190.
    HOGENOMi HOG000236379.
    HOVERGENi HBG053298.
    InParanoidi Q9GZU7.
    KOi K15731.
    OrthoDBi EOG71P2C3.
    PhylomeDBi Q9GZU7.
    TreeFami TF313556.

    Enzyme and pathway databases

    SignaLinki Q9GZU7.

    Miscellaneous databases

    ChiTaRSi CTDSP1. human.
    EvolutionaryTracei Q9GZU7.
    GeneWikii CTDSP1.
    GenomeRNAii 58190.
    NextBioi 64884.
    PROi Q9GZU7.
    SOURCEi Search...

    Gene expression databases

    Bgeei Q9GZU7.
    CleanExi HS_CTDSP1.
    Genevestigatori Q9GZU7.

    Family and domain databases

    Gene3Di 3.40.50.1000. 1 hit.
    InterProi IPR011948. Dullard_phosphatase.
    IPR023214. HAD-like_dom.
    IPR004274. NIF.
    [Graphical view ]
    Pfami PF03031. NIF. 1 hit.
    [Graphical view ]
    SMARTi SM00577. CPDc. 1 hit.
    [Graphical view ]
    SUPFAMi SSF56784. SSF56784. 1 hit.
    TIGRFAMsi TIGR02251. HIF-SF_euk. 1 hit.
    PROSITEi PS50969. FCP1. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Complete nucleotide sequence and genomic structure of the human NRAMP1 gene region on chromosome region 2q35."
      Marquet S., Lepage P., Hudson T.J., Musser J.M., Schurr E.
      Mamm. Genome 11:755-762(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM 1).
    2. "A novel RNA polymerase II C-terminal domain phosphatase that preferentially dephosphorylates serine 5."
      Yeo M., Lin P.S., Dahmus M.E., Gill G.N.
      J. Biol. Chem. 278:26078-26085(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), NUCLEOTIDE SEQUENCE [MRNA] OF 50-260 (ISOFORM 2), FUNCTION, SUBCELLULAR LOCATION, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, INTERACTION WITH GTF2F1, MUTAGENESIS OF ASP-96 AND ASP-98.
    3. "Full-length cDNA libraries and normalization."
      Li W.B., Gruber C., Jessee J., Polayes D.
      Submitted (APR-2003) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
      Tissue: Placenta.
    4. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
      Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
      , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
      Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Tissue: Lymph.
    6. "Small CTD phosphatases function in silencing neuronal gene expression."
      Yeo M., Lee S.-K., Lee B., Ruiz E.C., Pfaff S.L., Gill G.N.
      Science 307:596-600(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, TISSUE SPECIFICITY, INTERACTION WITH REST.
    7. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    8. "Structure and mechanism of RNA polymerase II CTD phosphatases."
      Kamenski T., Heilmeier S., Meinhart A., Cramer P.
      Mol. Cell 15:399-407(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 77-261 IN COMPLEX WITH MAGNESIUM AND INHIBITOR.
    9. "Determinants for dephosphorylation of the RNA polymerase II C-terminal domain by Scp1."
      Zhang Y., Kim Y., Genoud N., Gao J., Kelly J.W., Pfaff S.L., Gill G.N., Dixon J.E., Noel J.P.
      Mol. Cell 24:759-770(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 77-256 OF MUTANT ASN-96 IN COMPLEX WITH SUBSTRATE PEPTIDES, SUBSTRATE SPECIFICITY.

    Entry informationi

    Entry nameiCTDS1_HUMAN
    AccessioniPrimary (citable) accession number: Q9GZU7
    Secondary accession number(s): C9IYG0, Q7Z5Q3, Q7Z5Q4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 13, 2001
    Last sequence update: March 1, 2001
    Last modified: October 1, 2014
    This is version 119 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome 2
      Human chromosome 2: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    6. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3