MolNFT v1 · #146511 · protein
Integrin alpha-V beta-8 in complex with the fabs 8B8 and 68
6DJP: “Integrin alpha-V beta-8 in complex with the fabs 8B8 and 68”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 16 pockets (best druggability 0.85). MolNFT v1 #146511 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6DJP
- Type
- protein
- Length
- 1,393 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-V; Integrin beta-8; 8B8 heavy chain Fab; 8B8 light chain Fab; 68 heavy…
- UniProt
- P06756, P26012
- Ligands
- NAG, MAN, BMA
- Pockets
- 16 · best druggability 0.85
Structure
electron microscopy · 6 distinct chains · 9% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-V | protein | 593 | 4% helix, 43% strand | P06756 |
| B | Integrin beta-8 | protein | 353 | 24% helix, 29% strand | P26012 |
| C | 8B8 heavy chain Fab | protein | 117 | 0% helix, 41% strand | — |
| D | 8B8 light chain Fab | protein | 107 | 3% helix, 36% strand | — |
| E | 68 heavy chain Fab | protein | 115 | 8% helix, 47% strand | — |
| F | 68 light chain Fab | protein | 108 | 0% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B, E
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.85 | 0.87 | 158 | empty |
| 2 | 735 | 0.83 | 0.86 | 113 | empty |
| 3 | 566 | 0.81 | 0.87 | 84 | empty |
| 4 | 758 | 0.80 | 0.84 | 109 | empty |
| 5 | 817 | 0.79 | 0.83 | 123 | empty |
Interfaces
7 interfaces between chains.
- A–B · 341 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 301 Ų buried · 0 hydrogen bonds · protein-protein
- E–F · 276 Ų buried · 0 hydrogen bonds · protein-protein
- B–E · 122 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 110 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan (N-glycosylation).
Compared structures
- 6DJP · Integrin alpha-v beta-8 in complex with the Fabs 8B8 and 68 · the same entry in another collection · chain F against F, 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 0.96
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 P06756
- Every structure of UniProt P26012
- Elsewhere: RCSB PDB 6DJP · PDBe 6DJP · UniProt P06756 · UniProt P26012
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