MolNFT v1 · #7695 · protein

Glycyl endopeptidase-complex with benzyloxycarbonyl-leucine-valine- glycine-methylene covalently bound to cysteine 25

1GEC: “Glycyl endopeptidase-complex with benzyloxycarbonyl-leucine-valine- glycine-methylene covalently bound to…”. X-ray diffraction, 2 ligands (PHQ, 0HQ). MolNFT v1 #7695 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1GEC
Type: protein
Length: 219 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycyl endopeptidase; Benzyloxycarbonyl-leucine-valine-glycine-methylene inhibitor
EC: 3.4.22.25
UniProt: P05994
Ligands: PHQ, 0HQ

Structure

x-ray diffraction · 2 distinct chains · 25% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Glycyl endopeptidase (EC 3.4.22.25)	protein	216	25% helix, 23% strand	P05994
I	Benzyloxycarbonyl-leucine-valine-glycine-methylene inhibitor	protein	3	0% helix, 33% strand	—

Ligands and binding sites

PHQ · benzyl chlorocarbonate · ligand · chains E, I
0HQ · Diazomethane · ion · chains E, I

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

Interfaces

1 interface between chains.

E–I · 330 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

1GEC · Glycyl endopeptidase-complex with benzyloxycarbonyl-leucine-valine-glycine-methylene… · the same entry in another collection · chain E against E, TM-score 1.00
P05994 · AlphaFold monomer V2.0 prediction for papaya proteinase 4 (P05994) · a predicted model of the same protein · chain E against A, TM-score 0.98

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 P05994
Elsewhere: RCSB PDB 1GEC · PDBe 1GEC · UniProt P05994

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