MolNFT v1 · #70762 · protein

Structure of LMO2462, a listeria monocytogenes amidohydrolase family putative dipeptidase

3LU2 · LMO2462 protein: “Structure of LMO2462, a listeria monocytogenes amidohydrolase family putative dipeptidase”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.72). MolNFT v1 #70762 on GenesisL1: 3D structure, binding…

PDB: 3LU2
Type: protein
Length: 618 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: LMO2462 protein
UniProt: Q8Y4H9
Ligands: ZN
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	LMO2462 protein	protein	309	40% helix, 17% strand	Q8Y4H9

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	139	0.72	0.91	34	empty
2	119	0.45	0.77	22	ZN
3	113	0.42	0.77	23	ZN
4	93	0.38	0.76	12	empty

Interfaces

1 interface between chains.

A–B · 946 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 modified (engineered).

Compared structures

3LU2 · Structure of lmo2462, a Listeria monocytogenes amidohydrolase family putative dipeptidase · 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 Q8Y4H9
Elsewhere: RCSB PDB 3LU2 · PDBe 3LU2 · UniProt Q8Y4H9

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