Research workbench
Crystal structure of catechol 1,2-dioxygenase from burkholderia ambifaria
Analyse Crystal structure of catechol 1,2-dioxygenase from burkholderia ambifaria in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VXT
- Type
- protein
- Length
- 623 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catechol 1,2-dioxygenase
- UniProt
- B1Z4S0
- Ligands
- PTY, CAQ, FE, CL
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catechol 1,2-dioxygenase | protein | 311 | 28% helix, 21% strand | B1Z4S0 |
| B | Catechol 1,2-dioxygenase | protein | 312 | 28% helix, 21% strand | B1Z4S0 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · 2 copies · chains A, B
- CAQ · Catechol · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.84 | 0.85 | 57 | PTY |
| 2 | 58 | 0.69 | 0.96 | 18 | empty |
| 3 | 57 | 0.68 | 0.96 | 19 | empty |
| 4 | 201 | 0.53 | 0.78 | 29 | empty |
| 5 | 76 | 0.52 | 0.86 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3520 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 5VXT · Crystal structure of catechol 1,2-dioxygenase from Burkholderia ambifaria · 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 B1Z4S0
- Elsewhere: RCSB PDB 5VXT · PDBe 5VXT · UniProt B1Z4S0
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