MolNFT v1 · #155859 · protein

Turning an asparaginyl endopeptidase into a peptide ligase

6LKO: “Turning an asparaginyl endopeptidase into a peptide ligase”. X-ray diffraction, 2 ligands (SNN, NAG), 3 pockets (best druggability 0.53). MolNFT v1 #155859 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6LKO
Type: protein
Length: 408 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Asparaginyl endopeptidase
EC: 3.4.22.34
UniProt: A0A0P0QM28
Ligands: SNN, NAG
Pockets: 3 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Asparaginyl endopeptidase (EC 3.4.22.34)	protein	408	43% helix, 13% strand	A0A0P0QM28

Ligands and binding sites

SNN · L-3-aminosuccinimide · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
PEG · Di(hydroxyethyl)ether · additive · chains A

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

Pockets

3 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	138	0.53	0.81	22	empty
2	82	0.45	0.81	22	empty
3	120	0.40	0.75	19	empty

Modifications

Observed in the structure: 3 disulfide, 2 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).

Compared structures

6LKO · Turning an asparaginyl endopeptidase into a peptide ligase · 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 A0A0P0QM28
Elsewhere: RCSB PDB 6LKO · PDBe 6LKO · UniProt A0A0P0QM28

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