MolNFT v1 · #166217 · protein
Integrin alpha-V beta-8 in complex with pro-TGF-BETA1
6UJA: “Integrin alpha-V beta-8 in complex with pro-TGF-BETA1”. Electron microscopy, 5 ligands (NAG, MAN, BMA), 13 pockets (best druggability 0.79). MolNFT v1 #166217 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6UJA
- Type
- protein
- Length
- 1,128 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-V; Integrin beta-8; Transforming growth factor beta-1 proprotein
- UniProt
- P06756, P26012, P07200
- Ligands
- NAG, MAN, BMA, CA, MG
- Pockets
- 13 · best druggability 0.79
Structure
electron microscopy · 3 distinct chains · 13% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-V | protein | 593 | 4% helix, 42% strand | P06756 |
| B | Integrin beta-8 | protein | 359 | 22% helix, 31% strand | P26012 |
| D | Transforming growth factor beta-1 proprotein | protein | 176 | 23% helix, 36% strand | P07200 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
- CA · Calcium ion · metal · 5 copies · chains A, B
- MG · Magnesium ion · metal · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.79 | 0.85 | 58 | empty |
| 2 | 716 | 0.79 | 0.84 | 97 | empty |
| 3 | 1177 | 0.77 | 0.79 | 116 | empty |
| 4 | 330 | 0.61 | 0.78 | 42 | empty |
| 5 | 372 | 0.61 | 0.77 | 46 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1906 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 750 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 240 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 7 disulfide (N-glycosylation, disulfide).
Compared structures
- 6UJA · Integrin alpha-v beta-8 in complex with pro-TGF-beta1 · the same entry in another collection · chain B against B, TM-score 1.00
- P06756 · AlphaFold monomer V2.0 prediction for integrin alpha-V (P06756) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P26012 · AlphaFold monomer V2.0 prediction for integrin beta-8 (P26012) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P07200 · AlphaFold monomer V2.0 prediction for transforming growth factor beta-1 proprotein… · a predicted model of the same protein · chain D against A, TM-score 0.82
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 P26012
- Every structure of UniProt P07200
- Elsewhere: RCSB PDB 6UJA · PDBe 6UJA · UniProt P06756 · UniProt P26012 · UniProt P07200
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