MolNFT v1 · #55281 · protein
Crystal structure of biphenyl dioxygenase variant RR41 with dibenzofuran
2YFJ · Biphenyl dioxygenase subunit alpha: “Crystal structure of biphenyl dioxygenase variant RR41 with dibenzofuran”. X-ray diffraction, 3 ligands (FES, 1IT, FE2), 20 pockets (best druggability 0.79). MolNFT v1 #55281 on GenesisL1: 3D…
- PDB
- 2YFJ
- Type
- protein
- Length
- 3,678 residues
- Chains
- 12
- 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
- P37333, P37334
- Ligands
- FES, 1IT, FE2
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Biphenyl dioxygenase subunit alpha (EC 1.14.12.18) | protein | 433 | 35% helix, 25% strand | P37333 |
| B, D, F, H, J, L | Biphenyl dioxygenase subunit beta (EC 1.14.12.18) | protein | 180 | 24% helix, 39% strand | P37334 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 6 copies · chains A, C, E, G, I, K
- 1IT · Dibenzofuran · ligand · 3 copies · chains A, C, E
- FE2 · Fe (II) ion · metal · 6 copies · chains A, C, E, G, I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.79 | 0.81 | 93 | empty |
| 2 | 204 | 0.78 | 0.93 | 33 | 1IT |
| 3 | 219 | 0.78 | 0.91 | 35 | empty |
| 4 | 717 | 0.77 | 0.81 | 106 | empty |
| 5 | 334 | 0.76 | 0.87 | 58 | empty |
Interfaces
25 interfaces between chains.
- G–H · 1916 Ų buried · 35 hydrogen bonds · protein-protein
- K–L · 1895 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 1890 Ų buried · 32 hydrogen bonds · protein-protein
- I–J · 1878 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1868 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 2YFJ · Crystal structure of Biphenyl dioxygenase variant RR41 with dibenzofuran · the same entry in another collection · chain L against L, 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 P37333
- Every structure of UniProt P37334
- Elsewhere: RCSB PDB 2YFJ · PDBe 2YFJ · UniProt P37333 · UniProt P37334
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