Research workbench
Integrin ALPHAIIBBETA3 headpiece bound to a chimeric fibrinogen gamma chain peptide, lggakqrgdv
Analyse Integrin ALPHAIIBBETA3 headpiece bound to a chimeric fibrinogen gamma chain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VDR
- Type
- protein
- Length
- 1,347 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-iib; Integrin beta-3; Fibrinogen; Monoclonal antibody 10E5 heavy chain…
- UniProt
- P08514, P05106, Q53Y18
- Ligands
- MAN, NAG, CA, MG
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-iib | protein | 452 | 6% helix, 41% strand | P08514 |
| B | Integrin beta-3 | protein | 455 | 24% helix, 28% strand | P05106 |
| C | Fibrinogen | protein | 7 | 0% helix, 14% strand | Q53Y18 |
| H | Monoclonal antibody 10E5 heavy chain | protein | 219 | 5% helix, 52% strand | — |
| L | Monoclonal antibody 10E5 light chain | protein | 214 | 6% helix, 50% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- MG · Magnesium ion · metal · chains B, C
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.78 | 0.83 | 54 | empty |
| 2 | 655 | 0.74 | 0.80 | 59 | empty |
| 3 | 196 | 0.54 | 0.78 | 31 | GOL |
| 4 | 136 | 0.52 | 0.80 | 34 | empty |
| 5 | 65 | 0.50 | 0.85 | 13 | empty |
Interfaces
6 interfaces between chains.
- H–L · 1993 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1710 Ų buried · 22 hydrogen bonds · protein-protein
- A–H · 634 Ų buried · 10 hydrogen bonds · protein-protein
- A–L · 396 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 318 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 2VDR · Integrin AlphaIIbBeta3 Headpiece Bound to a chimeric Fibrinogen Gamma chain peptide… · the same entry in another collection · chain A against A, TM-score 1.00
- P08514 · AlphaFold monomer V2.0 prediction for integrin alpha-iib (P08514) · a predicted model of the same protein · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P08514
- Every structure of UniProt P05106
- Every structure of UniProt Q53Y18
- Elsewhere: RCSB PDB 2VDR · PDBe 2VDR · UniProt P08514 · UniProt P05106 · UniProt Q53Y18
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