Research workbench
Crystal structure of 2,2',3-trihydroxybiphenyl 1,2-dioxygenase from dibenzofuran-degrading sphingomonas wittichii strain RW1
Analyse Crystal structure of 2,2',3-trihydroxybiphenyl 1,2-dioxygenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VB0
- Type
- protein
- Length
- 1,156 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GLYOXALASE/BLEOMYCIN resistance PROTEIN/DIOXYGENASE
- EC
- 1.13.11.-
- UniProt
- A5VGW5
- Ligands
- FE2, SO4
- Pockets
- 14 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | GLYOXALASE/BLEOMYCIN resistance PROTEIN/DIOXYGENASE (EC 1.13.11.-) | protein | 289 | 22% helix, 39% strand | A5VGW5 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- P6G · Hexaethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.66 | 0.82 | 35 | FE2 |
| 2 | 281 | 0.66 | 0.82 | 35 | empty |
| 3 | 308 | 0.65 | 0.81 | 32 | empty |
| 4 | 275 | 0.65 | 0.81 | 35 | empty |
| 5 | 246 | 0.62 | 0.80 | 38 | FE2 |
Interfaces
3 interfaces between chains.
- B–C · 514 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 60 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 59 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3VB0 · Crystal structure of 2,2',3-trihydroxybiphenyl 1,2-dioxygenase from… · 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 A5VGW5
- Elsewhere: RCSB PDB 3VB0 · PDBe 3VB0 · UniProt A5VGW5
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