MolNFT v1 · #24133 · protein
Biphenyl dioxygenase (BPHA1A2) derived from rhodococcus sp. strain RHA1
1ULI · Biphenyl dioxygenase large subunit: “Biphenyl dioxygenase (BPHA1A2) derived from rhodococcus sp. strain RHA1”. X-ray diffraction, 2 ligands (FES, FE2), 20 pockets (best druggability 0.75). MolNFT v1 #24133 on GenesisL1: 3D…
- PDB
- 1ULI
- Type
- protein
- Length
- 1,806 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biphenyl dioxygenase large subunit; Biphenyl dioxygenase small subunit
- EC
- 1.14.12.18
- UniProt
- Q53122, Q53123
- Ligands
- FES, FE2
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Biphenyl dioxygenase large subunit (EC 1.14.12.18) | protein | 424 | 34% helix, 25% strand | Q53122 |
| B, F | Biphenyl dioxygenase small subunit (EC 1.14.12.18) | protein | 177 | 25% helix, 40% strand | Q53123 |
| C | Biphenyl dioxygenase large subunit (EC 1.14.12.18) | protein | 425 | 35% helix, 25% strand | Q53122 |
| D | Biphenyl dioxygenase small subunit (EC 1.14.12.18) | protein | 178 | 25% helix, 39% strand | Q53123 |
| E | Biphenyl dioxygenase large subunit (EC 1.14.12.18) | protein | 425 | 35% helix, 25% strand | Q53122 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, C, E
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, D, F, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.75 | 0.98 | 17 | empty |
| 2 | 58 | 0.74 | 0.99 | 17 | empty |
| 3 | 57 | 0.73 | 0.99 | 18 | empty |
| 4 | 618 | 0.70 | 0.78 | 82 | empty |
| 5 | 277 | 0.68 | 0.84 | 42 | empty |
Interfaces
12 interfaces between chains.
- C–D · 1851 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1851 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 1846 Ų buried · 33 hydrogen bonds · protein-protein
- C–E · 1712 Ų buried · 39 hydrogen bonds · protein-protein
- A–E · 1708 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 1ULI · Biphenyl dioxygenase (BphA1A2) derived from Rhodococcus sp. strain RHA1 · the same entry in another collection · chain F against F, TM-score 1.00
- Q53122 · AlphaFold monomer V2.0 prediction for biphenyl 2,3-dioxygenase subunit alpha (Q53122) · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q53123 · AlphaFold monomer V2.0 prediction for biphenyl 2,3-dioxygenase subunit beta (Q53123) · a predicted model of the same protein · chain B 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 Q53122
- Every structure of UniProt Q53123
- Elsewhere: RCSB PDB 1ULI · PDBe 1ULI · UniProt Q53122 · UniProt Q53123
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