Research workbench
Structure of complete ectodomain of integrin AIIBB3
Analyse Structure of complete ectodomain of integrin AIIBB3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FCS
- Type
- protein
- Length
- 3,099 residues
- Chains
- 4
- 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 · 10% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin, alpha 2B | protein | 913 | 4% helix, 48% strand | Q17R67 |
| B | Integrin beta-3 | protein | 680 | 17% helix, 27% strand | P05106 |
| C | Integrin, alpha 2B | protein | 903 | 4% helix, 47% strand | Q17R67 |
| D | Integrin beta-3 | protein | 603 | 19% helix, 27% strand | P05106 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains B, A, C, D
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A
- CA · Calcium ion · metal · 14 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
- IMD · Imidazole · additive · 6 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 886 | 0.79 | 0.81 | 90 | empty |
| 2 | 629 | 0.77 | 0.83 | 55 | empty |
| 3 | 663 | 0.76 | 0.82 | 56 | empty |
| 4 | 1128 | 0.76 | 0.78 | 96 | empty |
| 5 | 571 | 0.75 | 0.82 | 59 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3385 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 3113 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 321 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 71 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 3FCS · Structure of complete ectodomain of integrin aIIBb3 · 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 3FCS · PDBe 3FCS · UniProt Q17R67 · UniProt P05106
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