Research workbench
Resting protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 8.5
Analyse Resting protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 8.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WHO
- Type
- protein
- Length
- 1,309 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
- BCT, FE
- Pockets
- 17 · 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 | 12% helix, 32% strand | P00436 |
| B, F | Protocatechuate 3,4-dioxygenase beta chain (EC 1.13.11.3) | protein | 236 | 9% helix, 30% strand | P00437 |
| D | Protocatechuate 3,4-dioxygenase beta chain (EC 1.13.11.3) | protein | 237 | 9% helix, 30% strand | P00437 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · chains A
- FE · Fe (III) ion · metal · 3 copies · chains B, D, F
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 926 | 0.80 | 0.82 | 87 | BME |
| 2 | 792 | 0.79 | 0.83 | 75 | empty |
| 3 | 927 | 0.79 | 0.81 | 76 | BME |
| 4 | 487 | 0.75 | 0.84 | 46 | empty |
| 5 | 445 | 0.75 | 0.84 | 49 | empty |
Interfaces
15 interfaces between chains.
- C–D · 3693 Ų buried · 66 hydrogen bonds · protein-protein
- A–B · 3647 Ų buried · 63 hydrogen bonds · protein-protein
- E–F · 3626 Ų buried · 63 hydrogen bonds · protein-protein
- D–F · 338 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 331 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 4WHO · Resting Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 8.5 · 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 B 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 4WHO · PDBe 4WHO · UniProt P00436 · UniProt P00437
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