Research workbench
Crystal structure of integrin alpha V beta 6 head
Analyse Crystal structure of integrin alpha V beta 6 head in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FFG
- Type
- protein
- Length
- 839 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-V; Integrin beta-6
- UniProt
- P06756, P18564
- Ligands
- NAG, MAN, BMA, CA, SO4
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-V | protein | 591 | 4% helix, 42% strand | P06756 |
| B | Integrin beta-6 | protein | 248 | 38% helix, 20% strand | P18564 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 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
- SO4 · Sulfate ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.82 | 0.85 | 63 | empty |
| 2 | 334 | 0.65 | 0.80 | 50 | empty |
| 3 | 165 | 0.45 | 0.75 | 22 | empty |
| 4 | 58 | 0.44 | 0.83 | 14 | empty |
| 5 | 101 | 0.38 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1703 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 5FFG · Crystal structure of integrin alpha V beta 6 head · the same entry in another collection · chain A against A, TM-score 1.00
- P18564 · AlphaFold monomer V2.0 prediction for integrin beta-6 (P18564) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P06756 · AlphaFold monomer V2.0 prediction for integrin alpha-V (P06756) · a predicted model of the same protein · chain A 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 P06756
- Every structure of UniProt P18564
- Elsewhere: RCSB PDB 5FFG · PDBe 5FFG · UniProt P06756 · UniProt P18564
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