MolNFT v1 · #24134 · protein
Biphenyl dioxygenase (BPHA1A2) in complex with the substrate
1ULJ · Biphenyl dioxygenase large subunit: “Biphenyl dioxygenase (BPHA1A2) in complex with the substrate”. X-ray diffraction, 3 ligands (FES, BNL, FE2), 20 pockets (best druggability 0.76). MolNFT v1 #24134 on GenesisL1: 3D structure…
- PDB
- 1ULJ
- Type
- protein
- Length
- 1,807 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, BNL, FE2
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Biphenyl dioxygenase large subunit (EC 1.14.12.18) | protein | 425 | 35% 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 | 33% helix, 26% 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, 24% strand | Q53122 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, C, E
- BNL · Biphenyl · ligand · 3 copies · chains A, C, E
- FE2 · Fe (II) ion · metal · 3 copies · chains A, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.76 | 0.98 | 18 | BNL |
| 2 | 71 | 0.74 | 0.98 | 18 | BNL |
| 3 | 101 | 0.73 | 0.95 | 28 | empty |
| 4 | 65 | 0.73 | 0.98 | 20 | BNL |
| 5 | 723 | 0.71 | 0.78 | 88 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1862 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1852 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 1835 Ų buried · 34 hydrogen bonds · protein-protein
- C–E · 1727 Ų buried · 38 hydrogen bonds · protein-protein
- A–E · 1720 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 1ULJ · Biphenyl dioxygenase (BphA1A2) in complex with the substrate · the same entry in another collection · chain B against B, 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 1ULJ · PDBe 1ULJ · UniProt Q53122 · UniProt Q53123
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