Research workbench
Re-refinement of integrin ALPHAIIBBETA3 headpiece bound to antagonist tirofiban
Analyse Re-refinement of integrin ALPHAIIBBETA3 headpiece bound to antagonist tirofiban in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VDM
- Type
- protein
- Length
- 1,341 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-iib; Integrin beta-3; Monoclonal antibody 10E5 heavy chain; Monoclonal…
- UniProt
- P08514, P05106
- Ligands
- AGG, MAN, NAG, CA, MG
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-iib | protein | 452 | 6% helix, 43% strand | P08514 |
| B | Integrin beta-3 | protein | 456 | 24% helix, 28% strand | P05106 |
| H | Monoclonal antibody 10E5 heavy chain | protein | 219 | 7% helix, 51% strand | — |
| L | Monoclonal antibody 10E5 light chain | protein | 214 | 6% helix, 50% strand | — |
Ligands and binding sites
- AGG · Tirofiban · ligand · chains A, B
- 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
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.78 | 0.83 | 54 | empty |
| 2 | 674 | 0.75 | 0.81 | 58 | empty |
| 3 | 314 | 0.56 | 0.76 | 42 | empty |
| 4 | 228 | 0.54 | 0.77 | 40 | GOL |
| 5 | 293 | 0.52 | 0.74 | 46 | empty |
Interfaces
4 interfaces between chains.
- H–L · 2006 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1722 Ų buried · 25 hydrogen bonds · protein-protein
- A–H · 625 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 399 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 2VDM · Re-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antagonist Tirofiban · 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
- P05106 · AlphaFold monomer V2.0 prediction for integrin beta-3 (P05106) · a predicted model of the same protein · chain B against A, TM-score 0.56
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
- Elsewhere: RCSB PDB 2VDM · PDBe 2VDM · UniProt P08514 · UniProt P05106
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