MolNFT v1 · #118889 · protein
Integrin alpha V beta 6 in complex with pro-TGF-beta
5FFO · Integrin alpha-V: “Integrin alpha V beta 6 in complex with pro-TGF-beta”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.80). MolNFT v1 #118889 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5FFO
- Type
- protein
- Length
- 2,909 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-V; Integrin beta-6; Transforming growth factor beta-1
- UniProt
- P06756, P18564, P01137
- Ligands
- NAG, MAN, BMA, CA, MN
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 7 distinct chains · 13% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-V | protein | 589 | 5% helix, 42% strand | P06756 |
| B, F | Integrin beta-6 | protein | 242 | 33% helix, 19% strand | P18564 |
| C | Transforming growth factor beta-1 | protein | 305 | 19% helix, 32% strand | P01137 |
| D | Transforming growth factor beta-1 | protein | 322 | 16% helix, 28% strand | P01137 |
| E | Integrin alpha-V | protein | 587 | 5% helix, 41% strand | P06756 |
| G | Transforming growth factor beta-1 | protein | 297 | 17% helix, 33% strand | P01137 |
| H | Transforming growth factor beta-1 | protein | 325 | 16% helix, 29% strand | P01137 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 32 copies · chains A, C, B, D, E, G, F, H
- MAN · alpha-D-mannopyranose · sugar · 22 copies · chains A, H, E, B
- BMA · beta-D-mannopyranose · sugar · 12 copies · chains A, B, E, F
- CA · Calcium ion · metal · 8 copies · chains A, E
- MN · Manganese (II) ion · metal · 6 copies · chains B, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.80 | 0.96 | 36 | empty |
| 2 | 971 | 0.80 | 0.81 | 86 | empty |
| 3 | 139 | 0.78 | 0.96 | 38 | empty |
| 4 | 563 | 0.76 | 0.83 | 54 | empty |
| 5 | 1053 | 0.73 | 0.76 | 110 | empty |
Interfaces
10 interfaces between chains.
- G–H · 4361 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 4299 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1744 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1723 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 760 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 disulfide, 18 glycan (disulfide, N-glycosylation).
Compared structures
- 5FFO · Integrin alpha V beta 6 in complex with pro-TGF-beta · the same entry in another collection · chain H against H, TM-score 1.00
- P06756 · AlphaFold monomer V2.0 prediction for integrin alpha-V (P06756) · a predicted model of the same protein · chain E against A, TM-score 0.97
- P18564 · AlphaFold monomer V2.0 prediction for integrin beta-6 (P18564) · a predicted model of the same protein · chain B against A, TM-score 0.95
- P01137 · AlphaFold monomer V2.0 prediction for transforming growth factor beta-1 proprotein… · a predicted model of the same protein · chain G against A, TM-score 0.71
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
- Every structure of UniProt P01137
- Elsewhere: RCSB PDB 5FFO · PDBe 5FFO · UniProt P06756 · UniProt P18564 · UniProt P01137
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