MolNFT v1 · #32581 · protein
Crystal structure of wild-type protocatechuate 3,4-dioxygenase from acinetobacter sp. ADP1 in complex with 4-hydroxybenzoate
2BUR · Protocatechuate 3,4-dioxygenase alpha chain: “Crystal structure of wild-type protocatechuate 3,4-dioxygenase from acinetobacter sp. ADP1 in complex with…”. X-ray diffraction, 2 ligands (PHB, FE), 6 pockets (best druggability 0.54).…
- PDB
- 2BUR
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- 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
- P20371, P20372
- Ligands
- PHB, FE
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protocatechuate 3,4-dioxygenase alpha chain (EC 1.13.11.3) | protein | 202 | 14% helix, 28% strand | P20371 |
| B | Protocatechuate 3,4-dioxygenase beta chain (EC 1.13.11.3) | protein | 238 | 13% helix, 31% strand | P20372 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.54 | 0.82 | 25 | PHB |
| 2 | 92 | 0.52 | 0.84 | 24 | empty |
| 3 | 125 | 0.46 | 0.78 | 19 | empty |
| 4 | 74 | 0.37 | 0.77 | 21 | empty |
| 5 | 60 | 0.27 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3970 Ų buried · 64 hydrogen bonds · protein-protein
Compared structures
- 2BUR · Crystal Structure Of Wild-Type Protocatechuate 3,4-Dioxygenase from Acinetobacter Sp.… · the same entry in another collection · chain A against A, TM-score 1.00
- P20372 · AlphaFold monomer V2.0 prediction for protocatechuate 3,4-dioxygenase beta chain (P20372) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P20371 · AlphaFold monomer V2.0 prediction for protocatechuate 3,4-dioxygenase alpha chain (P20371) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P20371
- Every structure of UniProt P20372
- Elsewhere: RCSB PDB 2BUR · PDBe 2BUR · UniProt P20371 · UniProt P20372
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