MolNFT v1 · #108845 · protein
Metal ion and ligand binding of integrin
4WK0 · Integrin alpha-5: “Metal ion and ligand binding of integrin”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 10 pockets (best druggability 0.82). MolNFT v1 #108845 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4WK0
- Type
- protein
- Length
- 879 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-5; Integrin beta-1; Arg-gly-asp
- UniProt
- P08648, P05556
- Ligands
- NAG, MAN, BMA, CA, MG
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-5 | protein | 449 | 4% helix, 36% strand | P08648 |
| B | Integrin beta-1 | protein | 427 | 26% helix, 29% strand | P05556 |
| C | Arg-gly-asp | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
- CA · Calcium ion · metal · 6 copies · chains A, B
- MG · Magnesium ion · metal · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.82 | 0.87 | 66 | empty |
| 2 | 54 | 0.61 | 0.92 | 16 | empty |
| 3 | 59 | 0.60 | 0.91 | 20 | empty |
| 4 | 308 | 0.59 | 0.78 | 40 | empty |
| 5 | 225 | 0.57 | 0.79 | 29 | MG |
Interfaces
3 interfaces between chains.
- A–B · 1799 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 171 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 164 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 4WK0 · Metal Ion and Ligand Binding of Integrin · the same entry in another collection · chain A against A, TM-score 1.00
- P08648 · AlphaFold monomer V2.0 prediction for integrin alpha-5 (P08648) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P05556 · AlphaFold monomer V2.0 prediction for integrin beta-1 (P05556) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P08648
- Every structure of UniProt P05556
- Elsewhere: RCSB PDB 4WK0 · PDBe 4WK0 · UniProt P08648 · UniProt P05556
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