MolNFT v1 · #108849 · protein
Metal ion and ligand binding of integrin
4WK4 · Integrin alpha-5: “Metal ion and ligand binding of integrin”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 13 pockets (best druggability 0.83). MolNFT v1 #108849 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4WK4
- Type
- protein
- Length
- 893 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-5; Integrin beta-1; Ala-cys-arg-gly-asp-gly-TRP-cys
- UniProt
- P08648, P05556
- Ligands
- NAG, MAN, BMA, CA, MG
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-5 | protein | 450 | 4% helix, 35% strand | P08648 |
| B | Integrin beta-1 | protein | 435 | 26% helix, 27% strand | P05556 |
| C | Ala-cys-arg-gly-asp-gly-TRP-cys | protein | 8 | 0% helix, 25% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 6 copies · 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
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.83 | 0.88 | 70 | empty |
| 2 | 298 | 0.60 | 0.78 | 34 | empty |
| 3 | 57 | 0.59 | 0.91 | 22 | empty |
| 4 | 217 | 0.50 | 0.76 | 26 | empty |
| 5 | 211 | 0.50 | 0.75 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1734 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 278 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 220 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 4WK4 · 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 0.96
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 4WK4 · PDBe 4WK4 · UniProt P08648 · UniProt P05556
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