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Crystal structure of catechol 1,2-dioxygenase protein from burkholderia multivorans
Analyse Crystal structure of catechol 1,2-dioxygenase protein from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UMH
- Type
- protein
- Length
- 617 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catechol 1,2-dioxygenase
- EC
- 1.13.11.1
- UniProt
- A0A0H3KXJ8
- Ligands
- ZN, CA, CL
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catechol 1,2-dioxygenase (EC 1.13.11.1) | protein | 307 | 28% helix, 23% strand | A0A0H3KXJ8 |
| B | Catechol 1,2-dioxygenase (EC 1.13.11.1) | protein | 310 | 28% helix, 23% strand | A0A0H3KXJ8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · 2 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.85 | 0.85 | 54 | PG4, PG6, EDO |
| 2 | 62 | 0.69 | 0.96 | 18 | empty |
| 3 | 59 | 0.68 | 0.95 | 18 | empty |
| 4 | 238 | 0.59 | 0.79 | 33 | EDO |
| 5 | 67 | 0.52 | 0.86 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3303 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (additive adduct).
Compared structures
- 5UMH · Crystal Structure of Catechol 1,2-dioxygenase protein from Burkholderia multivorans · 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 A0A0H3KXJ8
- Elsewhere: RCSB PDB 5UMH · PDBe 5UMH · UniProt A0A0H3KXJ8
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