MolNFT v1 · #166219 · protein
Integrin alpha-V beta-8 in complex with the fabs C6-RGD3 and 11D12V2
6UJC: “Integrin alpha-V beta-8 in complex with the fabs C6-RGD3 and 11D12V2”. Electron microscopy, 5 ligands (NAG, MAN, BMA), 16 pockets (best druggability 0.77). MolNFT v1 #166219 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6UJC
- Type
- protein
- Length
- 1,184 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-V; Integrin beta-8; C6-RGD3 heavy chain Fab; C6-RGD3 light chain Fab
- UniProt
- P06756, P26012
- Ligands
- NAG, MAN, BMA, CA, MG
- Pockets
- 16 · best druggability 0.77
Structure
electron microscopy · 4 distinct chains · 11% helix, 40% 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 | 25% helix, 31% strand | P26012 |
| E | C6-RGD3 heavy chain Fab | protein | 115 | 8% helix, 52% strand | — |
| F | C6-RGD3 light chain Fab | protein | 117 | 3% helix, 47% strand | — |
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, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.77 | 0.84 | 60 | empty |
| 2 | 132 | 0.77 | 0.95 | 32 | empty |
| 3 | 369 | 0.75 | 0.86 | 60 | empty |
| 4 | 359 | 0.62 | 0.78 | 49 | empty |
| 5 | 259 | 0.60 | 0.79 | 36 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1954 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 761 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 731 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 718 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 319 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6UJC · Integrin alpha-v beta-8 in complex with the Fabs C6-RGD3 and 11D12v2 · the same entry in another collection · chain A against A, 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
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 6UJC · PDBe 6UJC · UniProt P06756 · UniProt P26012
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