Research workbench
Crystal structure of bphd, a C-C hydrolase from burkholderia xenovorans LB400
Analyse Crystal structure of bphd, a C-C hydrolase from burkholderia xenovorans LB400 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OG1
- Type
- protein
- Length
- 568 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
- EC
- 3.7.1.8
- UniProt
- P47229
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (EC 3.7.1.8) | protein | 285 | 46% helix, 20% strand | P47229 |
| B | 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (EC 3.7.1.8) | protein | 283 | 47% helix, 20% strand | P47229 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- EOH · Ethanol · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.74 | 0.89 | 43 | SO4 |
| 2 | 145 | 0.63 | 0.85 | 34 | empty |
| 3 | 52 | 0.56 | 0.90 | 16 | empty |
| 4 | 176 | 0.52 | 0.78 | 27 | EOH |
| 5 | 178 | 0.42 | 0.73 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1084 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2OG1 · Crystal Structure of BphD, a C-C hydrolase from Burkholderia xenovorans LB400 · the same entry in another collection · chain A against A, TM-score 1.00
- P47229 · AlphaFold monomer V2.0 prediction for 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase… · a predicted model of the same protein · chain B 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 P47229
- Elsewhere: RCSB PDB 2OG1 · PDBe 2OG1 · UniProt P47229
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