MolNFT v1 · #115494 · protein
Crystal structure of SZ348 in complex with S,S-cyclohexanediol
5CLK · Limonene-1,2-epoxide hydrolase: “Crystal structure of SZ348 in complex with S,S-cyclohexanediol”. X-ray diffraction, 4 ligands (3ZQ, K, NI), 4 pockets (best druggability 0.73). MolNFT v1 #115494 on GenesisL1: 3D structure, binding…
- PDB
- 5CLK
- Type
- protein
- Length
- 301 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Limonene-1,2-epoxide hydrolase
- EC
- 3.3.2.8
- UniProt
- Q9ZAG3
- Ligands
- 3ZQ, K, NI, CL
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 154 | 24% helix, 35% strand | Q9ZAG3 |
| B | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 147 | 29% helix, 37% strand | Q9ZAG3 |
Ligands and binding sites
- 3ZQ · (1S,2S)-cyclohexane-1,2-diol · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains A, B
- NI · Nickel (II) ion · metal · 3 copies · chains A
- CL · Chloride ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.73 | 0.96 | 20 | 3ZQ |
| 2 | 67 | 0.69 | 0.94 | 21 | 3ZQ |
| 3 | 88 | 0.37 | 0.76 | 18 | empty |
| 4 | 62 | 0.28 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1683 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 5CLK · Crystal structure of SZ348 in complex with S,S-cyclohexanediol · 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 Q9ZAG3
- Elsewhere: RCSB PDB 5CLK · PDBe 5CLK · UniProt Q9ZAG3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.