MolNFT v1 · #54511 · protein
Crystal structure of biphenyl dioxygenase from burkholderia xenovorans LB400
2XR8 · Biphenyl dioxygenase subunit alpha: “Crystal structure of biphenyl dioxygenase from burkholderia xenovorans LB400”. X-ray diffraction, 2 ligands (FES, FE2), 20 pockets (best druggability 0.88). MolNFT v1 #54511 on GenesisL1: 3D…
- PDB
- 2XR8
- Type
- protein
- Length
- 7,356 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 0.88
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 29% 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, 24% strand | P37333 |
| B, D, F, H, J, L, N, P, R, T, V, X | 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 · 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 | 811 | 0.88 | 0.92 | 96 | empty |
| 2 | 939 | 0.88 | 0.90 | 126 | empty |
| 3 | 838 | 0.88 | 0.90 | 105 | empty |
| 4 | 367 | 0.84 | 0.93 | 60 | FE2 |
| 5 | 239 | 0.80 | 0.93 | 52 | FE2 |
Interfaces
73 interfaces between chains.
- W–X · 1902 Ų buried · 32 hydrogen bonds · protein-protein
- S–T · 1892 Ų buried · 34 hydrogen bonds · protein-protein
- O–P · 1886 Ų buried · 29 hydrogen bonds · protein-protein
- G–H · 1876 Ų buried · 40 hydrogen bonds · protein-protein
- E–F · 1876 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 2XR8 · Crystal structure of biphenyl dioxygenase from Burkholderia xenovorans LB400 · 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 2XR8 · PDBe 2XR8 · UniProt P37333 · UniProt P37334
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.