Research workbench
Crystal structure of wild-type protocatechuate 3,4-dioxygenase from acinetobacter sp. ADP1
Analyse Crystal structure of wild-type protocatechuate 3,4-dioxygenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BUM
- 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
- FE, OH
- Pockets
- 7 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 13% 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 | 13% helix, 28% strand | P20371 |
| B | Protocatechuate 3,4-dioxygenase beta chain (EC 1.13.11.3) | protein | 238 | 14% helix, 31% strand | P20372 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.54 | 0.84 | 23 | empty |
| 2 | 159 | 0.49 | 0.78 | 27 | empty |
| 3 | 117 | 0.47 | 0.79 | 22 | empty |
| 4 | 125 | 0.46 | 0.78 | 19 | empty |
| 5 | 55 | 0.31 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 3890 Ų buried · 63 hydrogen bonds · protein-protein
Compared structures
- 2BUM · Crystal Structure Of Wild-Type Protocatechuate 3,4-Dioxygenase from Acinetobacter Sp. ADP1 · 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 0.99
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 2BUM · PDBe 2BUM · UniProt P20371 · UniProt P20372
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