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Structure of H247A mutant peptidoglycan peptidase complex with penta peptide

Analyse Structure of H247A mutant peptidoglycan peptidase complex with penta peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6JN1
Type: protein
Length: 257 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.382
Source: Campylobacter jejuni; SYNTHETIC CONSTRUCT
Molecule: Peptidase M23; C0O-dal-dal
UniProt: A0A1J6PWI8
Ligands: ZN
Pockets: 2 · best druggability 0.52

Structure

x-ray diffraction · resolution 2.382 · 2 distinct chains · 12% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptidase M23	protein	254	12% helix, 42% strand	A0A1J6PWI8
B	C0O-dal-dal	protein	3	0% helix, 0% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · chains A, B

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	140	0.52	0.80	24	empty
2	179	0.48	0.76	23	empty

Interfaces

1 interface between chains.

A–B · 342 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 d-amino, 1 modified (D-amino acid, nonstandard).

Compared structures

6JN1 · Structure of H247A mutant peptidoglycan peptidase complex with penta 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 6JN1 · PDBe 6JN1 · UniProt A0A1J6PWI8

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