MolNFT v1 · #4390 · protein
Structure of catechol 1,2-dioxygenase from acinetobacter sp. ADP1 with bound 4-methylcatechol
1DMH: “Structure of catechol 1,2-dioxygenase from acinetobacter sp. ADP1 with bound 4-methylcatechol”. X-ray diffraction, 3 ligands (MCT, LIO, FE), 8 pockets (best druggability 0.83). MolNFT v1 #4390 on GenesisL1: 3D structure, binding…
- PDB
- 1DMH
- 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
- MCT, LIO, FE
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Catechol 1,2-dioxygenase (EC 1.13.11.1) | protein | 309 | 27% helix, 23% strand | P07773 |
Ligands and binding sites
- MCT · 4-methylcatechol · ligand · 2 copies · chains A, B
- LIO · [1-pentadecanoyl-2-decanoyl-glycerol-3-yl]phosphonyl choline · ligand · 2 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
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.83 | 0.84 | 58 | LIO |
| 2 | 73 | 0.71 | 0.96 | 19 | empty |
| 3 | 72 | 0.69 | 0.95 | 18 | empty |
| 4 | 225 | 0.55 | 0.77 | 28 | empty |
| 5 | 209 | 0.55 | 0.78 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 3426 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 1DMH · Structure of catechol 1,2-dioxygenase from acinetobacter sp. ADP1 with 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 0.99
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 1DMH · PDBe 1DMH · UniProt P07773
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