Research workbench
Crystal structure of glycoprotein VI in complex with collagen-peptide (GPO)3
Analyse Crystal structure of glycoprotein VI in complex with collagen-peptide (GPO)3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OU9
- Type
- protein
- Length
- 411 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platelet glycoprotein VI; (GPO)3
- UniProt
- Q9HCN6
- Ligands
- NAG, CL
- Pockets
- 2 · best druggability 0.27
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platelet glycoprotein VI | protein | 179 | 2% helix, 51% strand | Q9HCN6 |
| B | Platelet glycoprotein VI | protein | 169 | 2% helix, 53% strand | Q9HCN6 |
| C, D, E | (GPO)3 | protein | 21 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.27 | 0.74 | 10 | PG4 |
| 2 | 51 | 0.25 | 0.72 | 10 | PG4 |
Interfaces
8 interfaces between chains.
- D–E · 621 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 619 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 552 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 298 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 279 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified, 4 disulfide, 2 glycan (hydroxylation, disulfide, N-glycosylation).
Compared structures
- 5OU9 · Crystal structure of Glycoprotein VI in complex with collagen-peptide (GPO)3 · the same entry in another collection · chain B against B, TM-score 1.00
- Q9HCN6 · AlphaFold monomer V2.0 prediction for platelet glycoprotein VI (Q9HCN6) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 Q9HCN6
- Elsewhere: RCSB PDB 5OU9 · PDBe 5OU9 · UniProt Q9HCN6
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