MolNFT v1 · #80714 · protein
X-ray crystal structure of xenon-pressurized phenol hydroxylase from pseudomonas sp. OX1
3U52 · Phenol hydroxylase component phn: “X-ray crystal structure of xenon-pressurized phenol hydroxylase from pseudomonas sp. OX1”. X-ray diffraction, 4 ligands (FE, ZN, CU), 20 pockets (best druggability 0.80). MolNFT v1 #80714 on…
- PDB
- 3U52
- Type
- protein
- Length
- 1,869 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenol hydroxylase component phn; Phenol hydroxylase component phl; Phenol hydroxylase…
- UniProt
- Q84AQ2, Q84AQ4, Q84AQ1
- Ligands
- FE, ZN, CU, XE
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 64% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenol hydroxylase component phn | protein | 494 | 66% helix, 4% strand | Q84AQ2 |
| B | Phenol hydroxylase component phn | protein | 493 | 65% helix, 4% strand | Q84AQ2 |
| C | Phenol hydroxylase component phl | protein | 318 | 70% helix, 0% strand | Q84AQ4 |
| D | Phenol hydroxylase component phl | protein | 328 | 69% helix, 0% strand | Q84AQ4 |
| E, F | Phenol hydroxylase component pho | protein | 118 | 16% helix, 22% strand | Q84AQ1 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CU · Copper (II) ion · metal · 2 copies · chains A, C, B, D
- XE · Xenon · ion · 24 copies · chains A, C, B, D
- GOL · Glycerol · additive · 10 copies · chains A, C, B, D, F
- MPO · 3[N-morpholino]propane sulfonic acid · additive · chains B, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.80 | 0.98 | 23 | GOL, XE |
| 2 | 105 | 0.76 | 0.96 | 25 | FE, GOL, XE |
| 3 | 570 | 0.68 | 0.77 | 50 | empty |
| 4 | 111 | 0.64 | 0.88 | 19 | XE |
| 5 | 280 | 0.62 | 0.80 | 44 | empty |
Interfaces
10 interfaces between chains.
- B–D · 4155 Ų buried · 74 hydrogen bonds · protein-protein
- A–C · 3967 Ų buried · 74 hydrogen bonds · protein-protein
- A–E · 2149 Ų buried · 24 hydrogen bonds · protein-protein
- B–F · 2142 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 730 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3U52 · X-ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase from Pseudomonas sp. OX1 · 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 Q84AQ2
- Every structure of UniProt Q84AQ4
- Every structure of UniProt Q84AQ1
- Elsewhere: RCSB PDB 3U52 · PDBe 3U52 · UniProt Q84AQ2 · UniProt Q84AQ4 · UniProt Q84AQ1
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