MolNFT v1 · #153710 · protein

Structure of H247A mutant peptidoglycan peptidase complex with tetra- tri peptide

6JN0 · Peptidase M23: “Structure of H247A mutant peptidoglycan peptidase complex with tetra- tri peptide”. X-ray diffraction, 4 ligands (API, DAL, C0O), 2 pockets (best druggability 0.57). MolNFT v1 #153710 on GenesisL1: 3D structure…

PDB: 6JN0
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: API, DAL, C0O, ZN
Pockets: 2 · best druggability 0.57

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

API · 2,6-diaminopimelic acid · ligand · chains A
DAL · D-alanine · ligand · chains A
C0O · (~{Z},2~{R},6~{S})-2,6-bis(azanyl)hept-3-enedioic 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	385	0.57	0.74	33	API, DAL, C0O
2	139	0.49	0.78	24	empty

Compared structures

6JN0 · Structure of H247A mutant peptidoglycan peptidase complex with tetra-tri peptide · 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 6JN0 · PDBe 6JN0 · UniProt A0A1J6PWI8

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