MolNFT v1 · #65538 · protein
Crystal structure of the biphenyl dioxygenase in complex with biphenyl from comamonas testosteroni sp. strain B-356
3GZX · Biphenyl dioxygenase subunit alpha: “Crystal structure of the biphenyl dioxygenase in complex with biphenyl from comamonas testosteroni sp. strain…”. X-ray diffraction, 3 ligands (FES, BNL, FE2), 5 pockets (best druggability 0.73).…
- PDB
- 3GZX
- Type
- protein
- Length
- 626 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biphenyl dioxygenase subunit alpha; Biphenyl dioxygenase subunit beta
- EC
- 1.14.12.18
- UniProt
- Q46372, Q46373
- Ligands
- FES, BNL, FE2
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Biphenyl dioxygenase subunit alpha (EC 1.14.12.18) | protein | 440 | 31% helix, 25% strand | Q46372 |
| B | Biphenyl dioxygenase subunit beta (EC 1.14.12.18) | protein | 186 | 24% helix, 38% strand | Q46373 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · chains A
- BNL · Biphenyl · ligand · chains A
- FE2 · Fe (II) ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.73 | 0.85 | 55 | BNL |
| 2 | 292 | 0.61 | 0.79 | 42 | GOL |
| 3 | 215 | 0.55 | 0.78 | 32 | empty |
| 4 | 99 | 0.44 | 0.78 | 25 | empty |
| 5 | 53 | 0.31 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1764 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 3GZX · Crystal Structure of the Biphenyl Dioxygenase in complex with Biphenyl from Comamonas… · the same entry in another collection · chain A against A, TM-score 1.00
- Q46372 · AlphaFold monomer V2.0 prediction for biphenyl dioxygenase subunit alpha (Q46372) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q46373 · AlphaFold monomer V2.0 prediction for biphenyl dioxygenase subunit beta (Q46373) · a predicted model of the same protein · chain B 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 Q46372
- Every structure of UniProt Q46373
- Elsewhere: RCSB PDB 3GZX · PDBe 3GZX · UniProt Q46372 · UniProt Q46373
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