Research workbench
Resting Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 6.5
Analyse Resting Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 6.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WHP
- Type
- protein
- Length
- 1,313 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.541
- Source
- Pseudomonas putida
- Molecule
- Protocatechuate 3,4-dioxygenase alpha chain; Protocatechuate 3,4-dioxygenase beta chain
- EC
- 1.13.11.3
- UniProt
- P00436, P00437
- Ligands
- BCT, FE, SO4
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · resolution 1.541 · 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 | 12% helix, 32% strand | P00436 |
| F | Protocatechuate 3,4-dioxygenase beta chain (EC 1.13.11.3) | protein | 237 | 9% helix, 30% 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
- BCT · Bicarbonate ion · ligand · chains C
- FE · Fe (III) ion · metal · 3 copies · chains F, D, B
- SO4 · Sulfate ion · ion · 3 copies · chains E, F, C, D, A, B
- BME · Beta-mercaptoethanol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.79 | 0.81 | 78 | SO4 |
| 2 | 1000 | 0.79 | 0.81 | 86 | SO4 |
| 3 | 1071 | 0.79 | 0.80 | 85 | SO4 |
| 4 | 514 | 0.76 | 0.84 | 46 | empty |
| 5 | 460 | 0.76 | 0.84 | 58 | empty |
Interfaces
15 interfaces between chains.
- A–B · 3701 Ų buried · 61 hydrogen bonds · protein-protein
- C–D · 3672 Ų buried · 64 hydrogen bonds · protein-protein
- E–F · 3668 Ų buried · 61 hydrogen bonds · protein-protein
- F–D · 335 Ų buried · 6 hydrogen bonds · protein-protein
- F–B · 330 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 4WHP · Resting protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 6.5 · the same entry in another collection · chain F against F, 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 0.97
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 4WHP · PDBe 4WHP · UniProt P00436 · UniProt P00437
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