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Anhydride reaction intermediate trapped in protocatechuate 3,4- dioxygenase (pseudomonas putida) at pH 8.5
Analyse Anhydride reaction intermediate trapped in protocatechuate 3,4- dioxygenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WHR
- Type
- protein
- Length
- 1,311 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, 3NJ, FE, CL
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 4 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 | 14% helix, 33% strand | P00436 |
| D | Protocatechuate 3,4-dioxygenase beta chain (EC 1.13.11.3) | protein | 237 | 9% helix, 29% strand | P00437 |
| B | Protocatechuate 3,4-dioxygenase beta chain (EC 1.13.11.3) | protein | 238 | 9% helix, 29% strand | P00437 |
| F | Protocatechuate 3,4-dioxygenase beta chain (EC 1.13.11.3) | protein | 236 | 9% helix, 29% strand | P00437 |
Ligands and binding sites
- 3N8 · 4-fluorobenzene-1,2-diol · ligand · 14 copies · chains A, E, C, D, B, F
- 3NJ · 4-fluorooxepine-2,7-dione · ligand · chains A, B
- FE · Fe (III) ion · metal · 3 copies · chains D, B, F
- CL · Chloride ion · ion · chains F
- BME · Beta-mercaptoethanol · additive · 4 copies · chains A, B, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains D, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.79 | 0.83 | 73 | 3N8 |
| 2 | 996 | 0.79 | 0.81 | 76 | 3N8 |
| 3 | 1017 | 0.78 | 0.80 | 76 | 3N8, 3NJ |
| 4 | 587 | 0.76 | 0.82 | 49 | 3N8 |
| 5 | 470 | 0.75 | 0.84 | 49 | 3N8, TRS, BME |
Interfaces
15 interfaces between chains.
- A–B · 3687 Ų buried · 70 hydrogen bonds · protein-protein
- C–D · 3683 Ų buried · 67 hydrogen bonds · protein-protein
- E–F · 3636 Ų buried · 65 hydrogen bonds · protein-protein
- B–F · 328 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 321 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 4WHR · Anhydride reaction intermediate trapped in Protocatechuate 3,4-dioxygenase (pseudomonas… · 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 0.98
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 4WHR · PDBe 4WHR · UniProt P00436 · UniProt P00437
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