MolNFT v1 · #7246 · protein

Zinc peptidase from grifola frondosa

1G12 · Peptidyl-lys metalloendopeptidase: “Zinc peptidase from grifola frondosa”. X-ray diffraction, 2 ligands (MAN, ZN), 1 pocket (best druggability 0.32). MolNFT v1 #7246 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1G12
Type: protein
Length: 167 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptidyl-lys metalloendopeptidase
EC: 3.4.24.20
UniProt: P81054
Ligands: MAN, ZN
Pockets: 1 · best druggability 0.32

Structure

x-ray diffraction · 1 distinct chain · 57% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptidyl-lys metalloendopeptidase (EC 3.4.24.20)	protein	167	57% helix, 8% strand	P81054

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · chains A
ZN · Zinc ion · metal · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	50	0.32	0.77	18	empty

Modifications

Observed in the structure: 2 disulfide, 1 glycan (disulfide, O-glycosylation).

Compared structures

1G12 · Zinc peptidase from grifola frondosa · the same entry in another collection · chain A against A, TM-score 1.00
P81054 · AlphaFold monomer V2.0 prediction for peptidyl-lys metalloendopeptidase (P81054) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P81054
Elsewhere: RCSB PDB 1G12 · PDBe 1G12 · UniProt P81054

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