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URL: https://www.rcsb.org/annotations/2VDN

⇱ Annotations: 2VDN


👁 RCSB PDB
255,630
Structures from the PDB archive
1,062,058
Computed Structure Models (CSM)

 2VDN | pdb_00002vdn

Re-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antagonist Eptifibatide


Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
E [auth L]d2vdnl2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) automated matches (Mus musculus ) [TaxId: 10090 ], SCOPe (2.08)
E [auth L]d2vdnl1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin automated matches automated matches (Mus musculus ) [TaxId: 10090 ], SCOPe (2.08)
D [auth H]d2vdnh1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma (Mus musculus ) [TaxId: 10090 ], SCOPe (2.08)
Ad2vdna_ All beta proteins 7-bladed beta-propeller Integrin alpha N-terminal domain Integrin alpha N-terminal domain Integrin alpha N-terminal domain HUMAN (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
E [auth L]SCOP2B SuperfamilyImmunoglobulin (Ig) domain-like 8091539 3000071 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyPlexin repeat-like 8042732 3000415 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyvWA-like 8055554 3000832 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyIntegrin domains 8055552 3002062 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyIntegrin domains 8055552 3002062 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyIntegrin alpha N-terminal domain 8042728 3000314 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
E [auth L]Lipocaline2vdnL1 A: beta barrelsX: HTHH: NudixT: NudixF: LipocalinECOD (v294.2)
D [auth H]Copper-binde2vdnH1 A: beta barrelsX: Phage tail fiber protein trimerization domainH: beta-Prism IT: beta-Prism IF: Copper-bindECOD (v294.2)
D [auth H]Lipocaline2vdnH2 A: beta barrelsX: HTHH: NudixT: NudixF: LipocalinECOD (v294.2)
BPF26550e2vdnB1 A: beta barrelsX: amino-terminal domain of OmpATbH: amino-terminal domain of OmpATbT: amino-terminal domain of OmpATbF: PF26550ECOD (v294.2)
ALipocaline2vdnA1 A: beta barrelsX: HTHH: NudixT: NudixF: LipocalinECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
E [auth L]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
D [auth H]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
B3.30.1680.10 Alpha Beta 2-Layer Sandwich ligand-binding face of the semaphorins, domain 2 ligand-binding face of the semaphorins, domain 2CATH (4.3.0)
B2.60.40.1510 Mainly Beta Sandwich Immunoglobulin-like ntegrin, alpha v. Chain A, domain 3CATH (4.3.0)
B3.40.50.410 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold von Willebrand factor, type A domainCATH (4.3.0)
A2.130.10.130 Mainly Beta 7 Propeller Methylamine Dehydrogenase Chain HCATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

ChainProtein NameDescriptionOrganism NameGene Allele Name(s)Domain Name(s)Receptor TypeReceptor DescriptionProvenance Source
E [auth L]10E5 L-KAPPA Mus musculus (house mouse) IGKV14-100*01, IGKJ2*01, IGKC*01, IGKC*02 V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA IG FAB-GAMMA-2A_KAPPA IMGT (202622-0)
D [auth H]10E5 VH-CH1 Mus musculus (house mouse) IGHV14-3*02, IGHJ4*01, IGHG2A*01, IGHG2A*02 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-2A_KAPPA IMGT (202622-0)
INTEGRIN-ALPHA-IIB_BETA-3 INTEGRIN-BETA-3 Homo sapiens (human) BETA-3 P-LIKE-DOMAIN PSI, Y-LIKE-DOMAIN Hybrid-1, B-LIKE-DOMAIN BETA-1, Y-LIKE-DOMAIN Hybrid-2, E-LIKE-DOMAIN EGF-1 RPI INTEGRIN-ALPHA-IIB_BETA-3 IMGT (202622-0)
INTEGRIN-ALPHA-IIB_BETA-3 INTEGRIN-ALPHA-IIB Homo sapiens (human) ALPHA-IIB BP-LIKE-DOMAIN B-Propeller RPI INTEGRIN-ALPHA-IIB_BETA-3 IMGT (202622-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
E [auth L]Light ChainIGKV14 Kappaintegrin alpha-iibSAbDab (2026-06-12)
D [auth H]Heavy ChainIGHV14 -integrin alpha-iibSAbDab (2026-06-12)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
E [auth L]PF07654Immunoglobulin C1-set domain (C1-set)Immunoglobulin C1-set domainDomain
PF18372Integrin beta epidermal growth factor like domain 1 (I-EGF_1)Integrin beta epidermal growth factor like domain 1This is the I-EGF 1 domain found in several integrin betas such as integrin beta 1-7. Structural analysis reveal an epidermal growth factor-like (I-EGF) domains 1 and 2 [1]. EGF1 lacks one disulfide (C2-C4) relative to the integrin EGF 2, 3, and 4 do ...This is the I-EGF 1 domain found in several integrin betas such as integrin beta 1-7. Structural analysis reveal an epidermal growth factor-like (I-EGF) domains 1 and 2 [1]. EGF1 lacks one disulfide (C2-C4) relative to the integrin EGF 2, 3, and 4 domains, this allows the C-terminal end of EGF1 to flex remarkably relative to its N-terminal end [14].
Domain
PF00362Integrin beta chain VWA domain (Integrin_beta)Integrin beta chain VWA domainIntegrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer [1]. This domain corresponds to the integrin beta VWA domain. Domain
PF17205Integrin plexin domain (PSI_integrin)Integrin plexin domainThis short disulphide rich domain is found at the N-terminus of integrin beta chains. Domain
PF01839FG-GAP repeat (FG-GAP)FG-GAP repeat- Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
E [auth L]MONOCLONAL ANTIBODY 10E5 LIGHT CHAIN-
D [auth H]MONOCLONAL ANTIBODY 10E5 HEAVY CHAIN---
EPTIFIBATIDE---
INTEGRIN BETA-3
INTEGRIN ALPHA-IIB

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
E [auth L]IPR003597Immunoglobulin C1-setDomain
E [auth L]IPR013783Immunoglobulin-like foldHomologous Superfamily
E [auth L]IPR036179Immunoglobulin-like domain superfamilyHomologous Superfamily
E [auth L]IPR007110Immunoglobulin-like domainDomain
E [auth L]IPR050380Immune Recognition and Response ModulatorsFamily
E [auth L]IPR003006Immunoglobulin/major histocompatibility complex, conserved siteConserved Site
IPR033760Integrin beta N-terminalDomain
IPR036465von Willebrand factor A-like domain superfamilyHomologous Superfamily
IPR032695Integrin domain superfamilyHomologous Superfamily
IPR002369Integrin beta subunit, VWA domainDomain
IPR040622Integrin beta, epidermal growth factor-like domain 1Domain
IPR036349Integrin beta tail domain superfamilyHomologous Superfamily
IPR014836Integrin beta subunit, cytoplasmic domainDomain
IPR012896Integrin beta subunit, tailDomain
IPR013111Epidermal growth factor-like domain, extracellularDomain
IPR057073Integrin beta, epidermal growth factor-like domain 2Domain
IPR015812Integrin beta subunitFamily
IPR057243Integrins beta, I-EGF domain, conserved siteConserved Site
IPR016201PSI domainDomain
IPR013517FG-GAP repeatRepeat
IPR013519Integrin alpha beta-propellorRepeat
IPR000413Integrin alpha chainFamily
IPR048286Integrin alpha, third immunoglobulin-like domainDomain
IPR013649Integrin alpha, first immunoglubulin-like domainDomain
IPR028994Integrin alpha, N-terminalHomologous Superfamily
IPR048285Integrin alpha, second immunoglobulin-like domainDomain
IPR032695Integrin domain superfamilyHomologous Superfamily
IPR018184Integrin alpha chain, C-terminal cytoplasmic region, conserved siteConserved Site

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
P05106
P08514

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
HRG Parent Component: ARG

MPT
NH2 AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100

:  L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.