MolNFT v1 · #115450 · protein
Crystal structure of SZ348 in complex with cyclopentene oxide
5CK6 · Limonene-1,2-epoxide hydrolase: “Crystal structure of SZ348 in complex with cyclopentene oxide”. X-ray diffraction, 3 ligands (3ZS, K, NI), 5 pockets (best druggability 0.73). MolNFT v1 #115450 on GenesisL1: 3D structure, binding…
- PDB
- 5CK6
- Type
- protein
- Length
- 300 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
- 3ZS, K, NI
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 154 | 27% helix, 36% strand | Q9ZAG3 |
| B | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 146 | 29% helix, 37% strand | Q9ZAG3 |
Ligands and binding sites
- 3ZS · (1R,5S)-6-oxabicyclo[3.1.0]hexane · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.73 | 0.97 | 21 | 3ZS |
| 2 | 123 | 0.43 | 0.76 | 29 | empty |
| 3 | 59 | 0.29 | 0.74 | 18 | empty |
| 4 | 55 | 0.29 | 0.74 | 13 | empty |
| 5 | 58 | 0.27 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1709 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5CK6 · Crystal structure of SZ348 in complex with cyclopentene oxide · 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 5CK6 · PDBe 5CK6 · UniProt Q9ZAG3
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