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Crystal structure of biphenyl 2,3-dioxygenase from sphingomonas yanoikuyae B1 bound to biphenyl
Analyse Crystal structure of biphenyl 2,3-dioxygenase from sphingomonas yanoikuyae B1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GBX
- Type
- protein
- Length
- 1,854 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biphenyl 2,3-dioxygenase alpha subunit; Biphenyl 2,3-dioxygenase beta subunit
- UniProt
- A2TC87, A2TC88
- Ligands
- FES, BNL, ZN, FE
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Biphenyl 2,3-dioxygenase alpha subunit | protein | 449 | 33% helix, 25% strand | A2TC87 |
| B, D, F | Biphenyl 2,3-dioxygenase beta subunit | protein | 170 | 23% helix, 41% strand | A2TC88 |
| C | Biphenyl 2,3-dioxygenase alpha subunit | protein | 446 | 33% helix, 24% strand | A2TC87 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, C, E
- BNL · Biphenyl · ligand · 3 copies · chains A, C, E
- ZN · Zinc ion · metal · 9 copies · chains B, D, F
- FE · Fe (III) ion · metal · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 381 | 0.80 | 0.89 | 37 | empty |
| 2 | 104 | 0.79 | 0.98 | 23 | BNL |
| 3 | 593 | 0.78 | 0.84 | 79 | ZN |
| 4 | 98 | 0.78 | 0.98 | 21 | FE, BNL |
| 5 | 98 | 0.77 | 0.97 | 21 | FE, BNL |
Interfaces
12 interfaces between chains.
- A–B · 1778 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 1763 Ų buried · 32 hydrogen bonds · protein-protein
- C–E · 1714 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1712 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1669 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 2GBX · Crystal Structure of Biphenyl 2,3-Dioxygenase from Sphingomonas yanoikuyae B1 Bound to… · the same entry in another collection · chain A 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 A2TC87
- Every structure of UniProt A2TC88
- Elsewhere: RCSB PDB 2GBX · PDBe 2GBX · UniProt A2TC87 · UniProt A2TC88
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