› 2vdm

X-ray diffraction
2.9Å resolution

Re-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antagonist Tirofiban

Released:
DOI: 10.2210/pdb2vdm/pdb
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PDB entry 2vdm coloured by chain, front view.
PDB entry 2vdm coloured by chain, side view.
PDB entry 2vdm coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for distinctive recognition of fibrinogen gammaC peptide by the platelet integrin alphaIIbbeta3.
Springer TA, Zhu J, Xiao T
OpenAccess logo J Cell Biol 182 791-800 (2008)
PMID: 18710925

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-209200 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (6 distinct):
Integrin alpha-IIb heavy chain Chain: A
Molecule details ›
Chain: A
Length: 452 amino acids
Theoretical weight: 49.03 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P08514 (Residues: 32-483; Coverage: 45%)
Gene names: GP2B, ITGA2B, ITGAB
Sequence domains: FG-GAP repeat
Structure domains: Integrin alpha, N-terminal
Integrin beta-3 Chain: B
Molecule details ›
Chain: B
Length: 461 amino acids
Theoretical weight: 50.97 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P05106 (Residues: 27-487; Coverage: 61%)
Gene names: GP3A, ITGB3
Sequence domains:
Structure domains:
MONOCLONAL ANTIBODY 10E5 HEAVY CHAIN Chain: H
MONOCLONAL ANTIBODY 10E5 LIGHT CHAIN Chain: L

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
5 bound ligands:
Ligand GOL 2 x GOL
Ligand CA 6 x CA
Ligand NAG 3 x NAG
Ligand AGG 1 x AGG
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: CHESS BEAMLINE A1
Spacegroup: P3221
Unit cell:
a: 148.577Å b: 148.577Å c: 177.239Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.169 0.167 0.206
Expression system: Cricetulus griseus

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Citations

19 review citations

Integrin inside-out signaling and the immunological synapse.
Springer et al. (2012)
18 more

20 mentions without citation

Current Challenges and Opportunities in Designing Protein-Protein Interaction Targeted Drugs.
Shin et al. (2020)
19 more

PDB-REDO

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