PDB entry 2vdm
View 2vdm on RCSB PDB site
Description: re-refinement of integrin alphaiibbeta3 headpiece bound to antagonist tirofiban
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 2.06 freeze date was dated
2011-07-13, with a file datestamp of
2011-05-31.
Experiment type: XRAY
Resolution: 2.9 Å
R-factor: 0.169
AEROSPACI score: 0.31
(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):
- Uniprot P08514 (0-451)
- conflict see remark 9 (281)
Domains in SCOPe 2.06: d2vdma_ - Chain 'B':
Compound: integrin beta-3
Species: Homo sapiens [TaxId:9606]
Database cross-references and differences (RAF-indexed):
- Chain 'H':
Compound: monoclonal antibody 10e5 heavy chain
Species: Mus musculus [TaxId:10090]
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.06: d2vdmh1 - Chain 'L':
Compound: monoclonal antibody 10e5 light chain
Species: Mus musculus [TaxId:10090]
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.06: d2vdml1, d2vdml2 - Heterogens: GOL, CA, NAG, AGG, MG, HOH
PDB Chain Sequences:
- Chain 'A':
Sequence; same for both SEQRES and ATOM records: (download)
>2vdmA (A:)
lnldpvqltfyagpngsqfgfsldfhkdshgrvaivvgaprtlgpsqeetggvflcpwra
eggqcpsllfdlrdetrnvgsqtlqtfkarqglgasvvswsdvivacapwqhwnvlekte
eaektpvgscflaqpesgrraeyspcrgntlsriyvendfswdkryceagfssvvtqage
lvlgapggyyflgllaqapvadifssyrpgillwhvssqslsfdssnpeyfdgywgysva
vgefdgdlntteyvvgaptwswtlgaveildsyyqrlhrlrgeqmasyfghsvavtdvng
dgrhdllvgaplymesradrklaevgrvylflqprgphalgapsllltgtqlygrfgsai
aplgdldrdgyndiavaapyggpsgrgqvlvflgqseglrsrpsqvldspfptgsafgfs
lrgavdiddngypdlivgayganqvavyraqp
- Chain 'B':
No sequence available.
- Chain 'H':
Sequence, based on SEQRES records: (download)
>2vdmH (H:)
evqlqqsgaelvkpgasvklsctasgfnikdtyvhwvkqrpeqglewigridpangytky
dpkfqgkatitadtssntaylqlssltsedtavyycvrplydyyamdywgqgtsvtvssa
kttapsvyplapvcgdttgssvtlgclvkgyfpepvtltwnsgslssgvhtfpavlqsdl
ytlsssvtvtsstwpsqsitcnvahpasstkvdkkieprgp
Sequence, based on observed residues (ATOM records): (download)
>2vdmH (H:)
evqlqqsgaelvkpgasvklsctasgfnikdtyvhwvkqrpeqglewigridpangytky
dpkfqgkatitadtssntaylqlssltsedtavyycvrplydyyamdywgqgtsvtvssa
kttapsvyplapvcttgssvtlgclvkgyfpepvtltwnsgslssgvhtfpavlqsdlyt
lsssvtvtsstwpsqsitcnvahpasstkvdkkieprgp
- Chain 'L':
Sequence; same for both SEQRES and ATOM records: (download)
>2vdmL (L:)
dilmtqspssmsvslgdtvsitchasqgissnigwlqqkpgksfmgliyygtnlvdgvps
rfsgsgsgadysltissldsedfadyycvqyaqlpytfgggtkleikradaaptvsifpp
sseqltsggasvvcflnnfypkdinvkwkidgserqngvlnswtdqdskdstysmsstlt
ltkdeyerhnsytceathktstspivksfnrnec