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Crystal structure of a pseudomonas putida prolyl-4-hydroxylase (P4H)
Analyse Crystal structure of a pseudomonas putida prolyl-4-hydroxylase (P4H) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J25
- Type
- protein
- Length
- 1,459 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein
- UniProt
- Q88CM1
- Ligands
- OGA, MN
- Pockets
- 18 · best druggability 0.69
Structure
x-ray diffraction · 8 distinct chains · 29% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein | protein | 181 | 29% helix, 30% strand | Q88CM1 |
| B | Putative uncharacterized protein | protein | 177 | 31% helix, 34% strand | Q88CM1 |
| C | Putative uncharacterized protein | protein | 179 | 30% helix, 32% strand | Q88CM1 |
| D | Putative uncharacterized protein | protein | 181 | 29% helix, 30% strand | Q88CM1 |
| E | Putative uncharacterized protein | protein | 184 | 29% helix, 35% strand | Q88CM1 |
| F | Putative uncharacterized protein | protein | 187 | 29% helix, 33% strand | Q88CM1 |
| G | Putative uncharacterized protein | protein | 184 | 27% helix, 34% strand | Q88CM1 |
| H | Putative uncharacterized protein | protein | 186 | 29% helix, 34% strand | Q88CM1 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MN · Manganese (II) ion · metal · 8 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
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.69 | 0.93 | 25 | MN, OGA |
| 2 | 795 | 0.66 | 0.74 | 87 | empty |
| 3 | 325 | 0.64 | 0.80 | 49 | empty |
| 4 | 399 | 0.61 | 0.77 | 38 | empty |
| 5 | 100 | 0.61 | 0.87 | 24 | MN, OGA |
Interfaces
10 interfaces between chains.
- A–H · 653 Ų buried · 13 hydrogen bonds · protein-protein
- C–G · 601 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 550 Ų buried · 12 hydrogen bonds · protein-protein
- B–H · 548 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 462 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4J25 · Crystal structure of a Pseudomonas putida prolyl-4-hydroxylase (P4H) · 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 Q88CM1
- Elsewhere: RCSB PDB 4J25 · PDBe 4J25 · UniProt Q88CM1
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