MolNFT v1 · #106457 · protein

Crystal structure of the LSD19-lasalocid a complex

4RZM · Epoxide hydrolase lasb: “Crystal structure of the LSD19-lasalocid a complex”. X-ray diffraction, 3 ligands (LSD, NA, CL), 5 pockets (best druggability 0.76). MolNFT v1 #106457 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4RZM
Type: protein
Length: 557 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Epoxide hydrolase lasb
EC: 5.5.1.-
UniProt: B6ZK72
Ligands: LSD, NA, CL
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Epoxide hydrolase lasb (EC 5.5.1.-)	protein	274	32% helix, 35% strand	B6ZK72
B	Epoxide hydrolase lasb (EC 5.5.1.-)	protein	283	32% helix, 34% strand	B6ZK72

Ligands and binding sites

LSD · Lasalocid A · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · 3 copies · chains A, B
CL · Chloride ion · ion
FMT · Formic acid · additive · 8 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	658	0.76	0.82	52	LSD, GOL
2	582	0.76	0.82	51	LSD, GOL
3	213	0.66	0.84	30	FMT
4	227	0.65	0.83	29	FMT
5	85	0.38	0.77	20	empty

Interfaces

1 interface between chains.

A–B · 431 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4RZM · Crystal structure of the Lsd19-lasalocid A complex · the same entry in another collection · chain A against A, TM-score 1.00
B6ZK72 · AlphaFold monomer V2.0 prediction for epoxide hydrolase lasb (B6ZK72) · a predicted model of the same protein · chain B 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 B6ZK72
Elsewhere: RCSB PDB 4RZM · PDBe 4RZM · UniProt B6ZK72

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