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Structure of catechol 1,2-dioxygenase from acinetobacter sp. ADP1 inhibited by bound mercury
Analyse Structure of catechol 1,2-dioxygenase from acinetobacter sp. ADP1 inhibited by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DLQ
- Type
- protein
- Length
- 618 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
- P07773
- Ligands
- LIO, HG, FE
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Catechol 1,2-dioxygenase (EC 1.13.11.1) | protein | 309 | 27% helix, 22% strand | P07773 |
Ligands and binding sites
- LIO · [1-pentadecanoyl-2-decanoyl-glycerol-3-yl]phosphonyl choline · ligand · 2 copies · chains A, B
- HG · Mercury (II) ion · metal · 6 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.84 | 0.84 | 56 | LIO |
| 2 | 68 | 0.70 | 0.96 | 20 | empty |
| 3 | 74 | 0.69 | 0.95 | 18 | empty |
| 4 | 262 | 0.62 | 0.80 | 34 | empty |
| 5 | 255 | 0.58 | 0.78 | 31 | HG |
Interfaces
1 interface between chains.
- A–B · 3429 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 1DLQ · Structure of catechol 1,2-dioxygenase from acinetobacter sp. ADP1 inhibited by bound… · the same entry in another collection · chain A against A, TM-score 1.00
- P07773 · AlphaFold monomer V2.0 prediction for catechol 1,2-dioxygenase (P07773) · a predicted model of the same protein · chain B 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 P07773
- Elsewhere: RCSB PDB 1DLQ · PDBe 1DLQ · UniProt P07773
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