MolNFT v1 · #109816 · protein

Crystal structure of the L74F/M78V/I80V/L114F mutant of leh

4XDW · Limonene-1,2-epoxide hydrolase: “Crystal structure of the L74F/M78V/I80V/L114F mutant of leh”. X-ray diffraction, 17 pockets (best druggability 0.79). MolNFT v1 #109816 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4XDW
Type: protein
Length: 1,141 residues
Chains: 8
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
Pockets: 17 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Limonene-1,2-epoxide hydrolase (EC 3.3.2.8)	protein	145	32% helix, 37% strand	Q9ZAG3
E	Limonene-1,2-epoxide hydrolase (EC 3.3.2.8)	protein	142	33% helix, 38% strand	Q9ZAG3
G, H	Limonene-1,2-epoxide hydrolase (EC 3.3.2.8)	protein	141	33% helix, 38% strand	Q9ZAG3
F	Limonene-1,2-epoxide hydrolase (EC 3.3.2.8)	protein	137	34% helix, 40% strand	Q9ZAG3

Pockets

17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	622	0.79	0.85	72	empty
2	591	0.79	0.86	67	empty
3	57	0.72	0.97	17	empty
4	196	0.68	0.85	31	empty
5	133	0.66	0.87	27	empty

Interfaces

12 interfaces between chains.

A–B · 1574 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1570 Å² buried · 21 hydrogen bonds · protein-protein
E–F · 1462 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 1452 Å² buried · 14 hydrogen bonds · protein-protein
A–F · 205 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4XDW · Crystal Structure of the L74F/M78V/I80V/L114F mutant of LEH · the same entry in another collection · chain D against D, TM-score 1.00
Q9ZAG3 · AlphaFold monomer V2.0 prediction for limonene-1,2-epoxide hydrolase (Q9ZAG3) · a predicted model of the same protein · chain F against A, TM-score 0.94

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 4XDW · PDBe 4XDW · UniProt Q9ZAG3

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