MolNFT v1 · #113420 · protein
Crystal structure of II9 variant of biphenyl dioxygenase from burkholderia xenovorans LB400 in complex with biphenyl
5AEW · Biphenyl dioxygenase subunit alpha: “Crystal structure of II9 variant of biphenyl dioxygenase from burkholderia xenovorans LB400 in complex with…”. X-ray diffraction, 3 ligands (FES, BNL, FE2), 20 pockets (best druggability 0.88).…
- PDB
- 5AEW
- Type
- protein
- Length
- 7,368 residues
- Chains
- 24
- 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, BNL, FE2
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 9 distinct chains · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S | Biphenyl dioxygenase subunit alpha (EC 1.14.12.18) | protein | 433 | 33% helix, 24% strand | P37333 |
| B, D, N | Biphenyl dioxygenase subunit beta (EC 1.14.12.18) | protein | 183 | 25% helix, 38% strand | P37334 |
| F | Biphenyl dioxygenase subunit beta (EC 1.14.12.18) | protein | 184 | 26% helix, 39% strand | P37334 |
| H, P, R, V | Biphenyl dioxygenase subunit beta (EC 1.14.12.18) | protein | 181 | 24% helix, 39% strand | P37334 |
| J | Biphenyl dioxygenase subunit beta (EC 1.14.12.18) | protein | 175 | 25% helix, 40% strand | P37334 |
| L, T | Biphenyl dioxygenase subunit beta (EC 1.14.12.18) | protein | 182 | 24% helix, 38% strand | P37334 |
| U | Biphenyl dioxygenase subunit alpha (EC 1.14.12.18) | protein | 430 | 32% helix, 22% strand | P37333 |
| W | Biphenyl dioxygenase subunit alpha (EC 1.14.12.18) | protein | 432 | 31% helix, 24% strand | P37333 |
| X | Biphenyl dioxygenase subunit beta (EC 1.14.12.18) | protein | 180 | 24% helix, 34% strand | P37334 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 12 copies · chains A, C, E, G, I, K, M, O, Q, S, U, W
- BNL · Biphenyl · ligand · 9 copies · chains C, E, I, K, M, O, Q, S, W
- FE2 · Fe (II) ion · metal · 12 copies · chains A, C, E, G, I, K, M, O, Q, S, U, W
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 | 838 | 0.88 | 0.90 | 108 | empty |
| 2 | 609 | 0.87 | 0.93 | 111 | empty |
| 3 | 706 | 0.86 | 0.90 | 93 | empty |
| 4 | 425 | 0.85 | 0.93 | 67 | FE2 |
| 5 | 356 | 0.83 | 0.92 | 66 | FE2 |
Interfaces
69 interfaces between chains.
- W–X · 1893 Ų buried · 33 hydrogen bonds · protein-protein
- I–J · 1871 Ų buried · 28 hydrogen bonds · protein-protein
- U–V · 1867 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 1855 Ų buried · 25 hydrogen bonds · protein-protein
- O–P · 1848 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5AEW · Crystal structure of II9 variant of Biphenyl dioxygenase from Burkholderia xenovorans… · the same entry in another collection · chain J against J, 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 5AEW · PDBe 5AEW · UniProt P37333 · UniProt P37334
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