MolNFT v1 · #114977 · protein
The crystal structure of viral collagen prolyl hydroxylase vcph from paramecium bursaria chlorella virus-1 - 2OG complex
5C5T · Prolyl 4-hydroxylase: “The crystal structure of viral collagen prolyl hydroxylase vcph from paramecium bursaria chlorella virus-1…”. X-ray diffraction, 3 ligands (AKG, ZN, MN), 3 pockets (best druggability 0.67). MolNFT v1 #114977…
- PDB
- 5C5T
- Type
- protein
- Length
- 360 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl 4-hydroxylase
- UniProt
- Q84406
- Ligands
- AKG, ZN, MN
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl 4-hydroxylase | protein | 181 | 22% helix, 33% strand | Q84406 |
| B | Prolyl 4-hydroxylase | protein | 179 | 22% helix, 32% strand | Q84406 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.67 | 0.96 | 20 | AKG, ZN |
| 2 | 73 | 0.61 | 0.90 | 24 | AKG, ZN |
| 3 | 181 | 0.44 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 234 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5C5T · The crystal structure of viral collagen prolyl hydroxylase vCPH from Paramecium Bursaria… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q84406
- Elsewhere: RCSB PDB 5C5T · PDBe 5C5T · UniProt Q84406
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