MolNFT v1 · #113419 · protein
Crystal structure of II9 variant of biphenyl dioxygenase from burkholderia xenovorans LB400
5AEU · Biphenyl dioxygenase subunit alpha: “Crystal structure of II9 variant of biphenyl dioxygenase from burkholderia xenovorans LB400”. X-ray diffraction, 2 ligands (FES, FE2), 20 pockets (best druggability 0.88). MolNFT v1 #113419 on…
- PDB
- 5AEU
- Type
- protein
- Length
- 2,461 residues
- Chains
- 8
- 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 0.88
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Biphenyl dioxygenase subunit alpha (EC 1.14.12.18) | protein | 433 | 33% helix, 24% strand | P37333 |
| B | Biphenyl dioxygenase subunit beta (EC 1.14.12.18) | protein | 183 | 27% helix, 39% strand | P37334 |
| D, F, H | Biphenyl dioxygenase subunit beta (EC 1.14.12.18) | protein | 182 | 24% helix, 38% strand | P37334 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains A, C, E, G
- FE2 · Fe (II) ion · metal · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1158 | 0.88 | 0.89 | 134 | empty |
| 2 | 230 | 0.80 | 0.93 | 38 | FE2 |
| 3 | 97 | 0.77 | 0.98 | 27 | empty |
| 4 | 481 | 0.77 | 0.84 | 42 | empty |
| 5 | 245 | 0.75 | 0.89 | 42 | FE2 |
Interfaces
19 interfaces between chains.
- C–D · 1858 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1850 Ų buried · 29 hydrogen bonds · protein-protein
- G–H · 1838 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1815 Ų buried · 24 hydrogen bonds · protein-protein
- C–G · 1688 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 5AEU · Crystal structure of II9 variant of Biphenyl dioxygenase from Burkholderia xenovorans… · the same entry in another collection · chain H against H, TM-score 1.00
- P37333 · AlphaFold monomer V2.0 prediction for biphenyl dioxygenase subunit alpha (P37333) · a predicted model of the same protein · chain C against A, 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 5AEU · PDBe 5AEU · UniProt P37333 · UniProt P37334
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