MolNFT v1 · #108774 · protein
Alkylperoxo reaction intermediate trapped in protocatechuate 3,4- dioxygenase (pseudomonas putida) at pH 6.5
4WHQ · Protocatechuate 3,4-dioxygenase alpha chain: “Alkylperoxo reaction intermediate trapped in protocatechuate 3,4- dioxygenase (pseudomonas putida) at pH 6.5”. X-ray diffraction, 7 ligands (3N8, BCT, 3N9), 20 pockets (best druggability…
- PDB
- 4WHQ
- Type
- protein
- Length
- 1,312 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protocatechuate 3,4-dioxygenase alpha chain; Protocatechuate 3,4-dioxygenase beta chain
- EC
- 1.13.11.3
- UniProt
- P00436, P00437
- Ligands
- 3N8, BCT, 3N9, FE, NA, CL, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, C | Protocatechuate 3,4-dioxygenase alpha chain (EC 1.13.11.3) | protein | 200 | 13% helix, 33% strand | P00436 |
| F | Protocatechuate 3,4-dioxygenase beta chain (EC 1.13.11.3) | protein | 236 | 9% helix, 28% strand | P00437 |
| D, B | Protocatechuate 3,4-dioxygenase beta chain (EC 1.13.11.3) | protein | 238 | 9% helix, 29% strand | P00437 |
Ligands and binding sites
- 3N8 · 4-fluorobenzene-1,2-diol · ligand · 17 copies · chains A, E, F, D, C, B
- BCT · Bicarbonate ion · ligand · 3 copies · chains F, E, B
- 3N9 · (6S)-4-fluoro-6-hydroperoxy-6-hydroxycyclohexa-2,4-dien-1-one · ligand · chains A, B
- FE · Fe (III) ion · metal · 3 copies · chains F, D, B
- NA · Sodium ion · metal · chains D
- CL · Chloride ion · ion · 3 copies · chains A, C
- SO4 · Sulfate ion · ion · chains E, C
- BME · Beta-mercaptoethanol · additive · 8 copies · chains F, C, D, B
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.80 | 0.81 | 75 | 3N8 |
| 2 | 970 | 0.80 | 0.81 | 76 | GOL, 3N8, 3N9 |
| 3 | 797 | 0.79 | 0.83 | 73 | 3N8 |
| 4 | 793 | 0.76 | 0.80 | 82 | BME, 3N8 |
| 5 | 598 | 0.75 | 0.82 | 52 | 3N8 |
Interfaces
15 interfaces between chains.
- A–B · 3716 Ų buried · 68 hydrogen bonds · protein-protein
- C–D · 3706 Ų buried · 65 hydrogen bonds · protein-protein
- E–F · 3669 Ų buried · 68 hydrogen bonds · protein-protein
- F–D · 326 Ų buried · 6 hydrogen bonds · protein-protein
- D–B · 320 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4WHQ · Alkylperoxo reaction intermediate trapped in Protocatechuate 3,4-dioxygenase (pseudomonas… · the same entry in another collection · chain B against B, TM-score 1.00
- P00437 · AlphaFold monomer V2.0 prediction for protocatechuate 3,4-dioxygenase beta chain (P00437) · a predicted model of the same protein · chain F against A, TM-score 1.00
- P00436 · AlphaFold monomer V2.0 prediction for protocatechuate 3,4-dioxygenase alpha chain (P00436) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P00436
- Every structure of UniProt P00437
- Elsewhere: RCSB PDB 4WHQ · PDBe 4WHQ · UniProt P00436 · UniProt P00437
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