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Crystal structure of II9 variant of biphenyl dioxygenase from burkholderia xenovorans LB400 in complex with biphenyl
Analyse Crystal structure of II9 variant of biphenyl dioxygenase from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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