MolNFT v1 · #114978 · protein
The crystal structure of viral collagen prolyl hydroxylase vcph from paramecium bursaria chlorella virus-1 - truncated construct
5C5U · Prolyl 4-hydroxylase: “The crystal structure of viral collagen prolyl hydroxylase vcph from paramecium bursaria chlorella virus-1…”. X-ray diffraction, 2 ligands (MN, UNX), 3 pockets (best druggability 0.60). MolNFT v1 #114978 on…
- PDB
- 5C5U
- Type
- protein
- Length
- 377 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl 4-hydroxylase
- UniProt
- Q84406
- Ligands
- MN, UNX
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl 4-hydroxylase | protein | 187 | 18% helix, 28% strand | Q84406 |
| B | Prolyl 4-hydroxylase | protein | 190 | 18% helix, 27% strand | Q84406 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 11 copies · chains A, B
- ACT · Acetate ion · additive · chains B
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 | 219 | 0.60 | 0.81 | 32 | ACT, UNX, MN |
| 2 | 180 | 0.60 | 0.82 | 32 | MN, UNX |
| 3 | 148 | 0.40 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 230 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5C5U · 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 5C5U · PDBe 5C5U · UniProt Q84406
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