MolNFT v1 · #108830 · protein
Metal ion and ligand binding of integrin
4WJK · Integrin alpha-5: “Metal ion and ligand binding of integrin”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 12 pockets (best druggability 0.82). MolNFT v1 #108830 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4WJK
- Type
- protein
- Length
- 876 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-5; Integrin beta-1
- UniProt
- P08648, P05556
- Ligands
- NAG, MAN, BMA, CA, MG
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-5 | protein | 452 | 4% helix, 35% strand | P08648 |
| B | Integrin beta-1 | protein | 424 | 27% helix, 29% strand | P05556 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A
- CA · Calcium ion · metal · 6 copies · chains A, B
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.82 | 0.87 | 67 | empty |
| 2 | 59 | 0.62 | 0.92 | 22 | empty |
| 3 | 146 | 0.56 | 0.82 | 22 | empty |
| 4 | 251 | 0.52 | 0.75 | 38 | empty |
| 5 | 153 | 0.48 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1803 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 4WJK · 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 0.98
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 4WJK · PDBe 4WJK · UniProt P08648 · UniProt P05556
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