Research workbench
Crystal structure of an atypical integrin
Analyse Crystal structure of an atypical integrin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OM1
- Type
- protein
- Length
- 3,689 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-V; Integrin beta-8
- UniProt
- P06756, P26012
- Ligands
- NAG, MAN, BMA, CA, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 8 distinct chains · 12% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-V | protein | 592 | 5% helix, 42% strand | P06756 |
| B | Integrin beta-8 | protein | 333 | 24% helix, 26% strand | P26012 |
| C | Integrin alpha-V | protein | 595 | 5% helix, 42% strand | P06756 |
| D | Integrin beta-8 | protein | 312 | 26% helix, 26% strand | P26012 |
| E | Integrin alpha-V | protein | 593 | 5% helix, 43% strand | P06756 |
| F | Integrin beta-8 | protein | 332 | 25% helix, 27% strand | P26012 |
| G | Integrin alpha-V | protein | 596 | 6% helix, 44% strand | P06756 |
| H | Integrin beta-8 | protein | 336 | 24% helix, 28% strand | P26012 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 62 copies · chains A, C, B, D, E, G, F, H
- MAN · alpha-D-mannopyranose · sugar · 29 copies · chains A, C, E, G
- BMA · beta-D-mannopyranose · sugar · 16 copies · chains A, C, E, G
- CA · Calcium ion · metal · 20 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 4 copies · chains B, D, F, H
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C, E, G, H
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.85 | 0.87 | 95 | empty |
| 2 | 1015 | 0.82 | 0.83 | 72 | empty |
| 3 | 666 | 0.79 | 0.84 | 64 | empty |
| 4 | 1068 | 0.79 | 0.81 | 107 | EDO |
| 5 | 301 | 0.69 | 0.83 | 56 | empty |
Interfaces
12 interfaces between chains.
- G–H · 2022 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1995 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1977 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1945 Ų buried · 23 hydrogen bonds · protein-protein
- E–G · 838 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 glycan, 35 disulfide (N-glycosylation, disulfide).
Compared structures
- 6OM1 · Crystal structure of an atypical integrin · the same entry in another collection · chain H against H, 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 F 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 6OM1 · PDBe 6OM1 · UniProt P06756 · UniProt P26012
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