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P70662

- LDB1_MOUSE

UniProt

P70662 - LDB1_MOUSE

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Protein
LIM domain-binding protein 1
Gene
Ldb1, Nli
Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Binds to the LIM domain of a wide variety of LIM domain-containing transcription factors. May regulate the transcriptional activity of LIM-containing proteins by determining specific partner interactions. Plays a role in the development of interneurons and motor neurons in cooperation with LHX3 and ISL1. Acts synergistically with LHX1/LIM1 in axis formation and activation of gene expression. Acts with LMO2 in the regulation of red blood cell development, maintaining erythroid precursors in an immature state.7 Publications

GO - Molecular functioni

  1. LIM domain binding Source: UniProtKB
  2. chromatin binding Source: MGI
  3. enhancer sequence-specific DNA binding Source: MGI
  4. enzyme binding Source: UniProtKB
  5. protein binding Source: UniProtKB
  6. protein homodimerization activity Source: UniProtKB
  7. protein self-association Source: MGI
  8. transcription cofactor activity Source: InterPro
  9. transcription factor binding transcription factor activity Source: MGI

GO - Biological processi

  1. Wnt signaling pathway Source: MGI
  2. anterior/posterior axis specification Source: MGI
  3. cellular component assembly Source: MGI
  4. cerebellar Purkinje cell differentiation Source: MGI
  5. cerebellum development Source: MGI
  6. epithelial structure maintenance Source: MGI
  7. gastrulation with mouth forming second Source: MGI
  8. hair follicle development Source: MGI
  9. head development Source: UniProtKB
  10. histone H3-K4 acetylation Source: BHF-UCL
  11. negative regulation of erythrocyte differentiation Source: UniProtKB
  12. negative regulation of transcription, DNA-templated Source: Ensembl
  13. neuron differentiation Source: UniProtKB
  14. positive regulation of cell adhesion Source: MGI
  15. positive regulation of hemoglobin biosynthetic process Source: BHF-UCL
  16. positive regulation of transcription from RNA polymerase II promoter Source: BHF-UCL
  17. primitive erythrocyte differentiation Source: BHF-UCL
  18. regulation of DNA-templated transcription, elongation Source: BHF-UCL
  19. somatic stem cell maintenance Source: MGI
  20. transcription from RNA polymerase II promoter Source: UniProtKB
  21. transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery Source: BHF-UCL
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Names & Taxonomyi

Protein namesi
Recommended name:
LIM domain-binding protein 1
Short name:
LDB-1
Alternative name(s):
Carboxyl-terminal LIM domain-binding protein 2
Short name:
CLIM-2
LIM domain-binding factor CLIM2
Short name:
mLdb1
Nuclear LIM interactor
Gene namesi
Name:Ldb1
Synonyms:Nli
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 19

Organism-specific databases

MGIiMGI:894762. Ldb1.

Subcellular locationi

Nucleus 3 Publications

GO - Cellular componenti

  1. nuclear chromatin Source: Ensembl
  2. nucleus Source: UniProtKB
  3. protein complex Source: UniProtKB
  4. transcription factor complex Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed By similarity
Chaini2 – 411410LIM domain-binding protein 1
PRO_0000084385Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserine By similarity

Post-translational modificationi

Ubiquitinated by RLIM/RNF12, leading to its degradation by the proteasome.1 Publication

Keywords - PTMi

Acetylation, Ubl conjugation

Proteomic databases

PaxDbiP70662.
PRIDEiP70662.

PTM databases

PhosphoSiteiP70662.

Expressioni

Tissue specificityi

Expression overlaps that of LIM domain-containing proteins. Expressed widely in the embryo with highest expression in several regions of the brain the central nervous system ganglia. Also expressed in fetal liver, lung, kidney, thymus and olfactory epithelium. Expressed in multiple adult tissues including heart, brain, liver, kidney, testis, lung and muscle and a diverse range of neuronal cell types, with expression highest in the pituitary gland and skin. Expressed in both embryonic and adult hemopoietic cells, including the erythroid lineage.4 Publications

Gene expression databases

ArrayExpressiP70662.
BgeeiP70662.
CleanExiMM_LDB1.
GenevestigatoriP70662.

Interactioni

Subunit structurei

Interacts with ESR1 By similarity. Forms homodimers and heterodimers. Interacts with and activates LHX1/LIM1. Interacts with the LIM domains of ISL1 and LMO2. Can assemble in a complex with LMO2 and TAL1/SCL but does not interact with TAL1/SCL directly. Strongly interacts with the LIM2 domain of LMX1A and more weakly with the LIM1 domain. Homodimerization is not required for, and does not effect, LMX1A-binding. Component of a nuclear TAL-1 complex composed at least of CBFA2T3, LDB1, TAL1 and TCF3. Interacts with LHX6 and LHX9. At neuronal promoters, forms a complex with LHX3 involved in the specification of interneurons, in motor neurons, it is displaced by ISL1 to form a ternary complex in which ISL1 contacts both LHX3 and LDB1.9 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
Cbfa2t3O549722EBI-6272082,EBI-8006703
Isl1P613723EBI-6272082,EBI-7988215
Lhx3P504815EBI-6272082,EBI-7988290
Tal1P220913EBI-6272082,EBI-8006437
Tcf4Q607222EBI-6272082,EBI-310070

Protein-protein interaction databases

BioGridi201125. 27 interactions.
IntActiP70662. 6 interactions.
MINTiMINT-2779250.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi307 – 3093
Beta strandi315 – 3217
Turni322 – 3243
Beta strandi325 – 3273
Turni329 – 3313
Beta strandi336 – 3449
Beta strandi346 – 3494
Beta strandi355 – 3573
Beta strandi359 – 3624
Turni369 – 3713
Beta strandi379 – 3846
Beta strandi387 – 3893
Helixi391 – 3933
Turni397 – 3993
Beta strandi408 – 4114

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1J2ONMR-A336-375[»]
1M3VNMR-A336-375[»]
1RUTX-ray1.30X336-375[»]
2JTNNMR-A331-375[»]
2L6YNMR-B336-348[»]
2L6ZNMR-C336-348[»]
2LXDNMR-A336-375[»]
4JCJX-ray3.00A/B/C300-411[»]
ProteinModelPortaliP70662.
SMRiP70662. Positions 336-363.

Miscellaneous databases

EvolutionaryTraceiP70662.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni336 – 37439LIM-binding domain (LID)
Add
BLAST

Domaini

The dimerization domain is located in the N-terminus.2 Publications

Sequence similaritiesi

Belongs to the LDB family.

Phylogenomic databases

eggNOGiNOG282114.
GeneTreeiENSGT00390000005639.
HOGENOMiHOG000030908.
HOVERGENiHBG000135.
InParanoidiP70662.
KOiK15617.
OMAiGSNSPWN.
PhylomeDBiP70662.
TreeFamiTF319923.

Family and domain databases

InterProiIPR029005. LIM-bd/SEUSS.
IPR002691. LIM-dom-bd.
[Graphical view]
PANTHERiPTHR10378. PTHR10378. 1 hit.
PfamiPF01803. LIM_bind. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 3 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: P70662-1) [UniParc]FASTAAdd to Basket

Also known as: Visvader-a

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

MSVGCACPGC SSKSFKLYSP KEPPNGNAFP PFHPGTMLDR DVGPTPMYPP    50
TYLEPGIGRH TPYGNQTDYR IFELNKRLQN WTEECDNLWW DAFTTEFFED 100
DAMLTITFCL EDGPKRYTIG RTLIPRYFRS IFEGGATELY YVLKHPKEAF 150
HSNFVSLDCD QGSMVTQHGK PMFTQVCVEG RLYLEFMFDD MMRIKTWHFS 200
IRQHRELIPR SILAMHAQDP QMLDQLSKNI TRCGLSNSTL NYLRLCVILE 250
PMQELMSRHK TYSLSPRDCL KTCLFQKWQR MVAPPAEPAR QQPSKRRKRK 300
MSGGSTMSSG GGNTNNSNSK KKSPASTFAL SSQVPDVMVV GEPTLMGGEF 350
GDEDERLITR LENTQFDAAN GIDDEDSFNN SPALGANSPW NSKPPSSQES 400
KSENPTSQAS Q 411
Length:411
Mass (Da):46,503
Last modified:September 11, 2007 - v2
Checksum:i47C53DFA23044580
GO
Isoform 2 (identifier: P70662-2) [UniParc]FASTAAdd to Basket

Also known as: Tran-b

The sequence of this isoform differs from the canonical sequence as follows:
     2-36: Missing.
     336-355: DVMVVGEPTLMGGEFGDEDE → VSISAFFSSGLPHCSPLTPV
     356-411: Missing.

Note: Due to intron retention. Lacks LIM-binding domain. Lacks ability to activate LIM domain-dependent transcription.

Show »
Length:320
Mass (Da):36,798
Checksum:iAE90F933828A17BC
GO
Isoform 3 (identifier: P70662-3) [UniParc]FASTAAdd to Basket

Also known as: Tran-a

The sequence of this isoform differs from the canonical sequence as follows:
     2-36: Missing.

Show »
Length:376
Mass (Da):42,910
Checksum:iFDE13F1E9984E4EA
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei2 – 3635Missing in isoform 2 and isoform 3.
VSP_027833Add
BLAST
Alternative sequencei336 – 35520DVMVV…GDEDE → VSISAFFSSGLPHCSPLTPV in isoform 2.
VSP_027834Add
BLAST
Alternative sequencei356 – 41156Missing in isoform 2.
VSP_027835Add
BLAST

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti262 – 2621Y → C in AAB96885. 1 Publication
Sequence conflicti334 – 3341V → A in AAB96885. 1 Publication
Sequence conflicti389 – 3902PW → QR in AAB96885. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U70375 mRNA. Translation: AAC52933.1.
U69270 mRNA. Translation: AAC52887.1.
U89488 mRNA. Translation: AAB96885.1.
AF030333 mRNA. Translation: AAB94131.1.
AF024524 Genomic DNA. Translation: AAC40064.1.
AB250383 mRNA. Translation: BAE95401.1.
BC013624 mRNA. Translation: AAH13624.1.
CCDSiCCDS50455.1. [P70662-1]
RefSeqiNP_001106879.1. NM_001113408.1. [P70662-1]
NP_034827.1. NM_010697.1.
UniGeneiMm.327442.

Genome annotation databases

EnsembliENSMUST00000026252; ENSMUSP00000026252; ENSMUSG00000025223.
ENSMUST00000056931; ENSMUSP00000053680; ENSMUSG00000025223.
ENSMUST00000137771; ENSMUSP00000114667; ENSMUSG00000025223.
ENSMUST00000156585; ENSMUSP00000118546; ENSMUSG00000025223. [P70662-1]
GeneIDi16825.
KEGGimmu:16825.
UCSCiuc008hrz.1. mouse. [P70662-1]
uc008hsa.1. mouse. [P70662-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U70375 mRNA. Translation: AAC52933.1 .
U69270 mRNA. Translation: AAC52887.1 .
U89488 mRNA. Translation: AAB96885.1 .
AF030333 mRNA. Translation: AAB94131.1 .
AF024524 Genomic DNA. Translation: AAC40064.1 .
AB250383 mRNA. Translation: BAE95401.1 .
BC013624 mRNA. Translation: AAH13624.1 .
CCDSi CCDS50455.1. [P70662-1 ]
RefSeqi NP_001106879.1. NM_001113408.1. [P70662-1 ]
NP_034827.1. NM_010697.1.
UniGenei Mm.327442.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1J2O NMR - A 336-375 [» ]
1M3V NMR - A 336-375 [» ]
1RUT X-ray 1.30 X 336-375 [» ]
2JTN NMR - A 331-375 [» ]
2L6Y NMR - B 336-348 [» ]
2L6Z NMR - C 336-348 [» ]
2LXD NMR - A 336-375 [» ]
4JCJ X-ray 3.00 A/B/C 300-411 [» ]
ProteinModelPortali P70662.
SMRi P70662. Positions 336-363.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 201125. 27 interactions.
IntActi P70662. 6 interactions.
MINTi MINT-2779250.

PTM databases

PhosphoSitei P70662.

Proteomic databases

PaxDbi P70662.
PRIDEi P70662.

Protocols and materials databases

DNASUi 16825.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000026252 ; ENSMUSP00000026252 ; ENSMUSG00000025223 .
ENSMUST00000056931 ; ENSMUSP00000053680 ; ENSMUSG00000025223 .
ENSMUST00000137771 ; ENSMUSP00000114667 ; ENSMUSG00000025223 .
ENSMUST00000156585 ; ENSMUSP00000118546 ; ENSMUSG00000025223 . [P70662-1 ]
GeneIDi 16825.
KEGGi mmu:16825.
UCSCi uc008hrz.1. mouse. [P70662-1 ]
uc008hsa.1. mouse. [P70662-2 ]

Organism-specific databases

CTDi 8861.
MGIi MGI:894762. Ldb1.

Phylogenomic databases

eggNOGi NOG282114.
GeneTreei ENSGT00390000005639.
HOGENOMi HOG000030908.
HOVERGENi HBG000135.
InParanoidi P70662.
KOi K15617.
OMAi GSNSPWN.
PhylomeDBi P70662.
TreeFami TF319923.

Miscellaneous databases

ChiTaRSi LDB1. mouse.
EvolutionaryTracei P70662.
NextBioi 290724.
PROi P70662.
SOURCEi Search...

Gene expression databases

ArrayExpressi P70662.
Bgeei P70662.
CleanExi MM_LDB1.
Genevestigatori P70662.

Family and domain databases

InterProi IPR029005. LIM-bd/SEUSS.
IPR002691. LIM-dom-bd.
[Graphical view ]
PANTHERi PTHR10378. PTHR10378. 1 hit.
Pfami PF01803. LIM_bind. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Interactions of the LIM-domain-binding factor Ldb1 with LIM homeodomain proteins."
    Agulnick A.D., Taira M., Breen J.J., Tanaka T., Dawid I.B., Westphal H.
    Nature 384:270-272(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), FUNCTION, INTERACTION WITH LHX1, TISSUE SPECIFICITY.
    Strain: Swiss Webster.
    Tissue: Embryo.
  2. "Nuclear LIM interactor, a rhombotin and LIM homeodomain interacting protein, is expressed early in neuronal development."
    Jurata L.W., Kenny D.A., Gill G.N.
    Proc. Natl. Acad. Sci. U.S.A. 93:11693-11698(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), FUNCTION, SUBCELLULAR LOCATION.
    Tissue: Embryo.
  3. "A family of LIM domain-associated cofactors confer transcriptional synergism between LIM and Otx homeodomain proteins."
    Bach I., Carriere C., Ostendorff H.P., Andersen B., Rosenfeld M.G.
    Genes Dev. 11:1370-1380(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), FUNCTION, TISSUE SPECIFICITY.
    Tissue: Embryonic head.
  4. "The LIM-domain binding protein Ldb1 and its partner LMO2 act as negative regulators of erythroid differentiation."
    Visvader J.E., Mao X., Fujiwara Y., Hahm K., Orkin S.H.
    Proc. Natl. Acad. Sci. U.S.A. 94:13707-13712(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INTERACTION WITH LMO2, IDENTIFICATION IN A COMPLEX WITH LMO2 AND TAL1.
    Tissue: Yolk sac.
  5. "Genomic structure and chromosomal localization of the mouse LIM domain-binding protein 1 gene, Ldb1."
    Yamashita T., Agulnick A.D., Copeland N.G., Gilbert D.J., Jenkins N.A., Westphal H.
    Genomics 48:87-92(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 129/Sv.
  6. "Spliced isoforms of LIM-domain-binding protein (CLIM/NLI/Ldb) lacking the LIM-interaction domain."
    Tran Y.H., Xu Z., Kato A., Mistry A.C., Goya Y., Taira M., Brandt S.J., Hirose S.
    J. Biochem. 140:105-119(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), FUNCTION, ALTERNATIVE SPLICING, TISSUE SPECIFICITY.
    Tissue: Heart.
  7. "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 3).
    Strain: FVB/N.
    Tissue: Mammary gland.
  8. "Functional analysis of the nuclear LIM domain interactor NLI."
    Jurata L.W., Gill G.N.
    Mol. Cell. Biol. 17:5688-5698(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH ISL1; LMO2 AND LMX1A, HOMODIMERIZATION, SUBCELLULAR LOCATION, IDENTIFICATION OF LIM-BINDING DOMAIN.
  9. "Interactions between LIM domains and the LIM domain-binding protein Ldb1."
    Breen J.J., Agulnick A.D., Westphal H., Dawid I.B.
    J. Biol. Chem. 273:4712-4717(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH LHX1, DOMAIN, HOMODIMERIZATION.
  10. "A brain region-specific gene product Lhx6.1 interacts with Ldb1 through tandem LIM-domains."
    Kimura N., Ueno M., Nakashima K., Taga T.
    J. Biochem. 126:180-187(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH LHX6.
    Tissue: Fetal brain.
  11. "Characterization of Lhx9, a novel LIM/homeobox gene expressed by the pioneer neurons in the mouse cerebral cortex."
    Bertuzzi S., Porter F.D., Pitts A., Kumar M., Agulnick A., Wassif C., Westphal H.
    Mech. Dev. 81:193-198(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH LHX9.
  12. "LIM factor Lhx3 contributes to the specification of motor neuron and interneuron identity through cell-type-specific protein-protein interactions."
    Thaler J.P., Lee S.K., Jurata L.W., Gill G.N., Pfaff S.L.
    Cell 110:237-249(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH LHX3 AND ISL1.
  13. "Ubiquitination-dependent cofactor exchange on LIM homeodomain transcription factors."
    Ostendorff H.P., Peirano R.I., Peters M.A., Schluter A., Bossenz M., Scheffner M., Bach I.
    Nature 416:99-103(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RLIM, UBIQUITINATION.
  14. "ETO2 coordinates cellular proliferation and differentiation during erythropoiesis."
    Goardon N., Lambert J.A., Rodriguez P., Nissaire P., Herblot S., Thibault P., Dumenil D., Strouboulis J., Romeo P.-H., Hoang T.
    EMBO J. 25:357-366(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN A NUCLEAR TAL-1 COMPLEX.
  15. "Structural basis for the recognition of ldb1 by the N-terminal LIM domains of LMO2 and LMO4."
    Deane J.E., Mackay J.P., Kwan A.H.Y., Sum E.Y.M., Visvader J.E., Matthews J.M.
    EMBO J. 22:2224-2233(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 336-375 IN COMPLEXES WITH LMO2 AND LMO4.
  16. "Tandem LIM domains provide synergistic binding in the LMO4:Ldb1 complex."
    Deane J.E., Ryan D.P., Sunde M., Maher M.J., Guss J.M., Visvader J.E., Matthews J.M.
    EMBO J. 23:3589-3598(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.3 ANGSTROMS) OF 336-375 IN COMPLEX WITH LMO4.

Entry informationi

Entry nameiLDB1_MOUSE
AccessioniPrimary (citable) accession number: P70662
Secondary accession number(s): O55204, Q1EQX2, Q71V68
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: September 11, 2007
Last modified: September 3, 2014
This is version 124 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi