MolNFT v1 · #153717 · protein

Structure of H216A mutant closed form peptidoglycan peptidase

6JN7 · Peptidase M23: “Structure of H216A mutant closed form peptidoglycan peptidase”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.80). MolNFT v1 #153717 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6JN7
Type: protein
Length: 786 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptidase M23
UniProt: A0A1J6PWI8
Ligands: ZN
Pockets: 10 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 13% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Peptidase M23	protein	262	13% helix, 41% strand	A0A1J6PWI8

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains A, B, C
TAR · D(-)-tartaric acid · additive · 3 copies · chains A, B, C

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

Pockets

10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	933	0.80	0.82	77	TAR
2	435	0.68	0.79	48	empty
3	653	0.67	0.76	67	empty
4	321	0.62	0.79	36	TAR
5	325	0.61	0.78	36	ZN, TAR

Interfaces

2 interfaces between chains.

A–B · 984 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 572 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6JN7 · Structure of H216A mutant closed form peptidoglycan peptidase · 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 6JN7 · PDBe 6JN7 · UniProt A0A1J6PWI8

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