Research workbench
Structure of headpiece of integrin AIIBB3 in open conformation
Analyse Structure of headpiece of integrin AIIBB3 in open conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FCU
- Type
- protein
- Length
- 2,725 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin, alpha 2B; Integrin beta-3
- UniProt
- Q17R67, P05106
- Ligands
- NAG, MAN, CA, MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin, alpha 2B | protein | 457 | 7% helix, 41% strand | Q17R67 |
| B, D, F | Integrin beta-3 | protein | 455 | 25% helix, 28% strand | P05106 |
| C | Integrin, alpha 2B | protein | 451 | 7% helix, 43% strand | Q17R67 |
| E | Integrin, alpha 2B | protein | 452 | 7% helix, 41% strand | Q17R67 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B, C, D, E, F
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, C, E
- CA · Calcium ion · metal · 18 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- CAC · Cacodylate ion · additive · 3 copies · chains B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 457 | 0.79 | 0.87 | 55 | empty |
| 2 | 1197 | 0.79 | 0.80 | 102 | empty |
| 3 | 702 | 0.78 | 0.82 | 54 | MG |
| 4 | 654 | 0.78 | 0.83 | 57 | MG |
| 5 | 697 | 0.77 | 0.82 | 55 | MG |
Interfaces
6 interfaces between chains.
- C–D · 1749 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1738 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1736 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 797 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 710 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 3FCU · Structure of headpiece of integrin aIIBb3 in open conformation · the same entry in another collection · 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 Q17R67
- Every structure of UniProt P05106
- Elsewhere: RCSB PDB 3FCU · PDBe 3FCU · UniProt Q17R67 · UniProt P05106
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