Research workbench
Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis
Analyse Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LMX
- Type
- protein
- Length
- 1,314 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- 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
- DHB, FE, SO4, CL
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.2 · 2 distinct chains · 11% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Protocatechuate 3,4-dioxygenase alpha chain (EC 1.13.11.3) | protein | 200 | 14% helix, 33% strand | P00436 |
| M, N, O | Protocatechuate 3,4-dioxygenase beta chain (EC 1.13.11.3) | protein | 238 | 9% helix, 29% strand | P00437 |
Ligands and binding sites
- DHB · 3,4-dihydroxybenzoic acid · ligand · 6 copies · chains A, M, O, N, B, C
- FE · Fe (III) ion · metal · 3 copies · chains M, N, O
- SO4 · Sulfate ion · ion · 11 copies · chains A, M, B, N, O, C
- CL · Chloride ion · ion · 6 copies · chains A, M, N, C, O
- BME · Beta-mercaptoethanol · additive · 23 copies · chains A, M, C, O, N, B
- GOL · Glycerol · additive · 10 copies · chains A, M, B, N, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.79 | 0.80 | 72 | BME, FE, DHB |
| 2 | 1011 | 0.78 | 0.80 | 77 | DHB, BME, GOL |
| 3 | 1040 | 0.78 | 0.80 | 76 | BME, FE, DHB |
| 4 | 522 | 0.77 | 0.84 | 48 | DHB |
| 5 | 445 | 0.76 | 0.84 | 46 | DHB |
Interfaces
15 interfaces between chains.
- C–O · 3708 Ų buried · 67 hydrogen bonds · protein-protein
- B–N · 3707 Ų buried · 68 hydrogen bonds · protein-protein
- A–M · 3703 Ų buried · 64 hydrogen bonds · protein-protein
- M–O · 360 Ų buried · 5 hydrogen bonds · protein-protein
- N–O · 354 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (additive adduct).
Compared structures
- 3LMX · Tyrosine 447 of protocatechuate 34,-dioxygenase controls efficient progress through… · the same entry in another collection · chain O against O, 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 M 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 3LMX · PDBe 3LMX · UniProt P00436 · UniProt P00437
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