Research workbench
Integrin ALAPHIIBBETA3 complex with EF5154
Analyse Integrin ALAPHIIBBETA3 complex with EF5154 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TPD
- Type
- protein
- Length
- 2,705 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-iib heavy chain; Integrin beta-3; Fab heavy chain; Fab light chain
- UniProt
- P08514, P05106
- Ligands
- IR7, NAG, BMA, CA, MG, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 12% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-iib heavy chain | protein | 457 | 6% helix, 41% strand | P08514 |
| B | Integrin beta-3 | protein | 466 | 23% helix, 29% strand | P05106 |
| C | Integrin alpha-iib heavy chain | protein | 453 | 6% helix, 41% strand | P08514 |
| D | Integrin beta-3 | protein | 471 | 25% helix, 29% strand | P05106 |
| E | Fab heavy chain | protein | 214 | 4% helix, 52% strand | — |
| F, L | Fab light chain | protein | 214 | 5% helix, 50% strand | — |
| H | Fab heavy chain | protein | 216 | 4% helix, 51% strand | — |
Ligands and binding sites
- IR7 · (4-{[2-oxo-4-(piperidin-4-yl)piperazin-1-yl]acetyl}phenoxy)acetic acid · ligand · 2 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 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 · 5 copies · chains A, 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 | 673 | 0.79 | 0.84 | 53 | empty |
| 2 | 673 | 0.78 | 0.83 | 57 | empty |
| 3 | 982 | 0.76 | 0.78 | 71 | IR7 |
| 4 | 706 | 0.75 | 0.80 | 54 | SO4 |
| 5 | 499 | 0.74 | 0.82 | 50 | empty |
Interfaces
11 interfaces between chains.
- E–F · 2052 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 2029 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1838 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1824 Ų buried · 24 hydrogen bonds · protein-protein
- C–E · 677 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7TPD · Integrin alpha IIB beta3 complex with EF5154 · the same entry in another collection · chain E against E, 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
- Elsewhere: RCSB PDB 7TPD · PDBe 7TPD · UniProt P08514 · UniProt P05106
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