MolNFT v1 · #188131 · protein
Integrin ALAPHIIBBETA3 complex with tirofiban
7TD8 · Integrin alpha-iib: “Integrin ALAPHIIBBETA3 complex with tirofiban”. X-ray diffraction, 6 ligands (AGG, NAG, BMA), 20 pockets (best druggability 0.79). MolNFT v1 #188131 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7TD8
- Type
- protein
- Length
- 2,701 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-iib; Integrin beta-3; Fab heavy chain; Fab light chain
- UniProt
- P08514, P05106
- Ligands
- AGG, NAG, BMA, CA, MG, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 14% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Integrin alpha-iib | protein | 453 | 6% helix, 41% strand | P08514 |
| B | Integrin beta-3 | protein | 466 | 24% helix, 29% strand | P05106 |
| D | Integrin beta-3 | protein | 471 | 25% helix, 28% strand | P05106 |
| E | Fab heavy chain | protein | 214 | 3% helix, 50% strand | — |
| F, L | Fab light chain | protein | 214 | 5% helix, 49% strand | — |
| H | Fab heavy chain | protein | 216 | 1% helix, 53% strand | — |
Ligands and binding sites
- AGG · Tirofiban · ligand · 2 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains A, C
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, H, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.79 | 0.84 | 55 | empty |
| 2 | 672 | 0.78 | 0.83 | 55 | empty |
| 3 | 1179 | 0.76 | 0.78 | 88 | SO4 |
| 4 | 876 | 0.74 | 0.78 | 66 | AGG |
| 5 | 566 | 0.73 | 0.81 | 62 | empty |
Interfaces
11 interfaces between chains.
- E–F · 2075 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 2027 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1809 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1805 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 695 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 7TD8 · Integrin alpha IIB beta3 complex with Tirofiban · the same entry in another collection · chain L against L, TM-score 1.00
- P08514 · AlphaFold monomer V2.0 prediction for integrin alpha-iib (P08514) · a predicted model of the same protein · chain C 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 0.91
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 7TD8 · PDBe 7TD8 · UniProt P08514 · UniProt P05106
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