MolNFT v1 · #107759 · protein
Crystal structure of alpha V beta 6
4UM8 · Integrin alpha-V: “Crystal structure of alpha V beta 6”. X-ray diffraction, 8 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.82). MolNFT v1 #107759 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4UM8
- Type
- protein
- Length
- 2,016 residues
- Chains
- 4
- 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, MG, NI, CL, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-V | protein | 591 | 4% helix, 41% strand | P06756 |
| B | Integrin beta-6 | protein | 423 | 24% helix, 28% strand | P18564 |
| C | Integrin alpha-V | protein | 588 | 4% helix, 42% strand | P06756 |
| D | Integrin beta-6 | protein | 414 | 23% helix, 29% strand | P18564 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 29 copies · chains A, C, B, D
- MAN · alpha-D-mannopyranose · sugar · 17 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 10 copies · chains A, C
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
- NI · Nickel (II) ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains A, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- CAC · Cacodylate ion · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 659 | 0.82 | 0.86 | 60 | empty |
| 2 | 666 | 0.80 | 0.85 | 61 | empty |
| 3 | 336 | 0.67 | 0.81 | 49 | empty |
| 4 | 683 | 0.66 | 0.75 | 54 | empty |
| 5 | 317 | 0.65 | 0.81 | 45 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2001 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1955 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 608 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 194 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
- 4UM8 · Crystal structure of alpha V beta 6 · the same entry in another collection · chain D against D, TM-score 1.00
- P06756 · AlphaFold monomer V2.0 prediction for integrin alpha-V (P06756) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P18564 · AlphaFold monomer V2.0 prediction for integrin beta-6 (P18564) · a predicted model of the same protein · chain D 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 P18564
- Elsewhere: RCSB PDB 4UM8 · PDBe 4UM8 · UniProt P06756 · UniProt P18564
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