MolNFT v1 · #177053 · protein

The crystal structure of peptidoglycan peptidase in complex with inhibitor 2

7E61 · Peptidase M23: “The crystal structure of peptidoglycan peptidase in complex with inhibitor 2”. X-ray diffraction, 2 ligands (HXF, ZN), 2 pockets (best druggability 0.54). MolNFT v1 #177053 on GenesisL1: 3D structure, binding sites…

PDB: 7E61
Type: protein
Length: 255 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptidase M23
UniProt: A0A1J6PWI8
Ligands: HXF, ZN
Pockets: 2 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 12% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptidase M23	protein	255	12% helix, 42% strand	A0A1J6PWI8

Ligands and binding sites

HXF · 2-[[(3S)-3-acetamido-4-[[(2R)-1-(oxidanylamino)-1-oxidanylidene-propan-2-yl]amino]-4-oxidanylidene-butyl]-(phenylmethyl)amino]ethanoic acid · ligand · chains A
ZN · Zinc ion · metal · chains A

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

Pockets

2 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	340	0.54	0.74	36	HXF
2	134	0.48	0.78	27	empty

Compared structures

7E61 · The crystal structure of peptidoglycan peptidase in complex with inhibitor 2 · 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 A0A1J6PWI8
Elsewhere: RCSB PDB 7E61 · PDBe 7E61 · UniProt A0A1J6PWI8

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