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Crystal structure of P4 variant of biphenyl dioxygenase from burkholderia xenovorans LB400
Analyse Crystal structure of P4 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
- 2XSO
- Type
- protein
- Length
- 7,382 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, FE2
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S, U, W | Biphenyl dioxygenase subunit alpha (EC 1.14.12.18) | protein | 433 | 34% helix, 25% strand | P37333 |
| B, D, F, H, J, L, P | Biphenyl dioxygenase subunit beta (EC 1.14.12.18) | protein | 183 | 25% helix, 38% strand | P37334 |
| N, R, T, V, X | Biphenyl dioxygenase subunit beta (EC 1.14.12.18) | protein | 181 | 24% helix, 39% 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
- 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 | 959 | 0.91 | 0.93 | 154 | empty |
| 2 | 948 | 0.88 | 0.90 | 121 | empty |
| 3 | 416 | 0.84 | 0.92 | 80 | empty |
| 4 | 158 | 0.82 | 0.98 | 28 | FE2 |
| 5 | 715 | 0.82 | 0.85 | 89 | empty |
Interfaces
63 interfaces between chains.
- U–V · 1889 Ų buried · 34 hydrogen bonds · protein-protein
- I–J · 1884 Ų buried · 30 hydrogen bonds · protein-protein
- W–X · 1878 Ų buried · 35 hydrogen bonds · protein-protein
- O–P · 1856 Ų buried · 31 hydrogen bonds · protein-protein
- Q–R · 1851 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 2XSO · Crystal structure of P4 variant of biphenyl dioxygenase from burkholderia xenovorans LB400 · the same entry in another collection · chain K against K, 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 2XSO · PDBe 2XSO · UniProt P37333 · UniProt P37334
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