MolNFT v1 · #65539 · protein
Crystal structure of the biphenyl dioxygenase from comamonas testosteroni sp. strain B-356
3GZY · Biphenyl dioxygenase subunit alpha: “Crystal structure of the biphenyl dioxygenase from comamonas testosteroni sp. strain B-356”. X-ray diffraction, 2 ligands (FES, FE2), 4 pockets (best druggability 0.72). MolNFT v1 #65539 on…
- PDB
- 3GZY
- 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, FE2
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Biphenyl dioxygenase subunit alpha (EC 1.14.12.18) | protein | 440 | 33% helix, 25% strand | Q46372 |
| B | Biphenyl dioxygenase subunit beta (EC 1.14.12.18) | protein | 186 | 24% helix, 36% strand | Q46373 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · chains A
- FE2 · Fe (II) ion · metal · chains A
- 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
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.72 | 0.84 | 56 | FE2 |
| 2 | 299 | 0.61 | 0.79 | 46 | empty |
| 3 | 217 | 0.51 | 0.76 | 21 | empty |
| 4 | 69 | 0.36 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1774 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 3GZY · Crystal Structure of the Biphenyl Dioxygenase from Comamonas testosteroni Sp. Strain B-356 · 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 3GZY · PDBe 3GZY · UniProt Q46372 · UniProt Q46373
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