Research workbench
Crystal structure of atypical integrin alphav BETA8 with protgf-BETA1 ligand peptide
Analyse Crystal structure of atypical integrin alphav BETA8 with protgf-BETA1 ligand… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OM2
- Type
- protein
- Length
- 1,853 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-V; Integrin beta-8; Protgf-BETA1 rgd peptide
- UniProt
- P06756, P26012
- Ligands
- GLY, NAG, MAN, BMA, CA, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 13% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-V | protein | 598 | 4% helix, 42% strand | P06756 |
| B | Integrin beta-8 | protein | 310 | 30% helix, 23% strand | P26012 |
| C | Integrin alpha-V | protein | 596 | 4% helix, 40% strand | P06756 |
| D | Integrin beta-8 | protein | 330 | 28% helix, 23% strand | P26012 |
| E | Protgf-BETA1 rgd peptide | protein | 10 | 0% helix, 0% strand | — |
| F | Protgf-BETA1 rgd peptide | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- GLY · Glycine · ligand · chains C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 29 copies · chains A, C, B, D
- MAN · alpha-D-mannopyranose · sugar · 18 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar · 9 copies · chains C, A
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, E, D, F
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.80 | 0.84 | 65 | empty |
| 2 | 793 | 0.78 | 0.82 | 82 | empty |
| 3 | 176 | 0.74 | 0.91 | 41 | empty |
| 4 | 139 | 0.67 | 0.88 | 21 | empty |
| 5 | 154 | 0.66 | 0.87 | 22 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1963 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1946 Ų buried · 27 hydrogen bonds · protein-protein
- B–E · 469 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 463 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 231 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
- 6OM2 · Crystal structure of atypical integrin alphaV beta8 with proTGF-beta1 ligand peptide · 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 C against A, TM-score 0.98
- P26012 · AlphaFold monomer V2.0 prediction for integrin beta-8 (P26012) · 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 P26012
- Elsewhere: RCSB PDB 6OM2 · PDBe 6OM2 · UniProt P06756 · UniProt P26012
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