MolNFT v1 · #21406 · protein
Crystal structure of 4-chlorocatechol 1,2-dioxygenase from rhodococcus opacus 1CP
1S9A: “Crystal structure of 4-chlorocatechol 1,2-dioxygenase from rhodococcus opacus 1CP”. X-ray diffraction, 4 ligands (HGP, BEZ, TAM), 7 pockets (best druggability 0.86). MolNFT v1 #21406 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1S9A
- Type
- protein
- Length
- 512 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chlorocatechol 1,2-dioxygenase
- EC
- 1.13.11.1
- UniProt
- O67987
- Ligands
- HGP, BEZ, TAM, FE
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Chlorocatechol 1,2-dioxygenase (EC 1.13.11.1) | protein | 256 | 25% helix, 27% strand | O67987 |
Ligands and binding sites
- HGP · (1-hexadecanoyl-2-tetradecanoyl-glycerol-3-yl) phosphonyl choline · ligand · 2 copies · chains A, B
- BEZ · Benzoic acid · ligand · 2 copies · chains A, B
- TAM · Tris(hydroxyethyl)aminomethane · ligand · 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.86 | 0.88 | 50 | HGP |
| 2 | 109 | 0.56 | 0.84 | 27 | BEZ |
| 3 | 160 | 0.50 | 0.78 | 25 | TAM |
| 4 | 132 | 0.47 | 0.78 | 21 | empty |
| 5 | 71 | 0.39 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2432 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 1S9A · Crystal Structure of 4-Chlorocatechol 1,2-dioxygenase from Rhodococcus opacus 1CP · the same entry in another collection · chain A against A, TM-score 1.00
- O67987 · AlphaFold monomer V2.0 prediction for chlorocatechol 1,2-dioxygenase (O67987) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O67987
- Elsewhere: RCSB PDB 1S9A · PDBe 1S9A · UniProt O67987
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