PDB entry 2vdn

View 2vdn on RCSB PDB site
Description: Re-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antagonist Eptifibatide
Class: cell adhesion/immune system
Keywords: cell adhesion-immune system complex, fibrinogen binding, platelet integrin alphaiibbeta3, glycoprotein, cell adhesion, membrane, integrin, receptor, antagonist, host-virus interaction, pyrrolidone carboxylic acid, transmembrane, phosphorylation, disease mutation, cleavage on pair of basic residues
Deposited on 2007-10-10, released 2008-09-02
The last revision prior to the SCOPe 2.08 freeze date was dated 2020-07-29, with a file datestamp of 2020-06-29.
Experiment type: XRAY
Resolution: 2.9 Å
R-factor: N/A
AEROSPACI score: 0.23 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: integrin alpha-IIb
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d2vdna_
  • Chain 'B':
    Compound: integrin beta-3
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: eptifibatide
    Species: synthetic construct, synthetic [TaxId:32630]
    Database cross-references and differences (RAF-indexed):
    • PDB 2VDN (0-6)
  • Chain 'H':
    Compound: monoclonal antibody 10e5 heavy chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 2VDN (0-220)
    Domains in SCOPe 2.08: d2vdnh1
  • Chain 'L':
    Compound: monoclonal antibody 10e5 light chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 2VDN (0-213)
    Domains in SCOPe 2.08: d2vdnl1, d2vdnl2
  • Heterogens: GOL, CA, NAG, MG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >2vdnA (A:)
lnldpvqltfyagpngsqfgfsldfhkdshgrvaivvgaprtlgpsqeetggvflcpwra
eggqcpsllfdlrdetrnvgsqtlqtfkarqglgasvvswsdvivacapwqhwnvlekte
eaektpvgscflaqpesgrraeyspcrgntlsriyvendfswdkryceagfssvvtqage
lvlgapggyyflgllaqapvadifssyrpgillwhvssqslsfdssnpeyfdgywgysva
vgefdgdlntteyvvgaptwswtlgaveildsyyqrlhrlrgeqmasyfghsvavtdvng
dgrhdllvgaplymesradrklaevgrvylflqprgphalgapsllltgtqlygrfgsai
aplgdldrdgyndiavaapyggpsgrgqvlvflgqseglrsrpsqvldspfptgsafgfs
lrgavdiddngypdlivgayganqvavyraqp

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    No sequence available.

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >2vdnH (H:)
evqlqqsgaelvkpgasvklsctasgfnikdtyvhwvkqrpeqglewigridpangytky
dpkfqgkatitadtssntaylqlssltsedtavyycvrplydyyamdywgqgtsvtvssa
kttapsvyplapvcgdttgssvtlgclvkgyfpepvtltwnsgslssgvhtfpavlqsdl
ytlsssvtvtsstwpsqsitcnvahpasstkvdkkieprgp

    Sequence, based on observed residues (ATOM records): (download) 
    >2vdnH (H:)
evqlqqsgaelvkpgasvklsctasgfnikdtyvhwvkqrpeqglewigridpangytky
dpkfqgkatitadtssntaylqlssltsedtavyycvrplydyyamdywgqgtsvtvssa
kttapsvyplapvcttgssvtlgclvkgyfpepvtltwnsgslssgvhtfpavlqsdlyt
lsssvtvtsstwpsqsitcnvahpasstkvdkkieprgp

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >2vdnL (L:)
dilmtqspssmsvslgdtvsitchasqgissnigwlqqkpgksfmgliyygtnlvdgvps
rfsgsgsgadysltissldsedfadyycvqyaqlpytfgggtkleikradaaptvsifpp
sseqltsggasvvcflnnfypkdinvkwkidgserqngvlnswtdqdskdstysmsstlt
ltkdeyerhnsytceathktstspivksfnrnec