MolNFT v1 · #164771 · protein
Prolyl hydroxylase (phd) involved in hypoxia sensing by dictyostelium discoideum
6T8M · Prolyl 4-hydroxylase subunit alpha: “Prolyl hydroxylase (phd) involved in hypoxia sensing by dictyostelium discoideum”. X-ray diffraction, 3 ligands (OGA, NI, CL), 8 pockets (best druggability 0.86). MolNFT v1 #164771 on GenesisL1…
- PDB
- 6T8M
- Type
- protein
- Length
- 607 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl 4-hydroxylase subunit alpha
- EC
- 1.14.11.-
- UniProt
- Q86KR9
- Ligands
- OGA, NI, CL
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl 4-hydroxylase subunit alpha (EC 1.14.11.-) | protein | 202 | 22% helix, 31% strand | Q86KR9 |
| B | Prolyl 4-hydroxylase subunit alpha (EC 1.14.11.-) | protein | 205 | 24% helix, 29% strand | Q86KR9 |
| C | Prolyl 4-hydroxylase subunit alpha (EC 1.14.11.-) | protein | 200 | 26% helix, 30% strand | Q86KR9 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 3 copies · chains A, B, C
- NI · Nickel (II) ion · metal · 5 copies · chains A, B, C
- CL · Chloride ion · ion · chains C
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.86 | 0.98 | 63 | NI, GOL, OGA |
| 2 | 260 | 0.70 | 0.84 | 30 | empty |
| 3 | 216 | 0.65 | 0.83 | 23 | empty |
| 4 | 94 | 0.63 | 0.89 | 25 | NI, OGA |
| 5 | 141 | 0.38 | 0.73 | 24 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1724 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 688 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6T8M · Prolyl Hydroxylase (PHD) involved in hypoxia sensing by Dictyostelium discoideum · the same entry in another collection · chain A against A, TM-score 1.00
- Q86KR9 · AlphaFold monomer V2.0 prediction for prolyl 4-hydroxylase subunit alpha (Q86KR9) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q86KR9
- Elsewhere: RCSB PDB 6T8M · PDBe 6T8M · UniProt Q86KR9
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