MolNFT v1 · #17802 · protein

Crystal structure of the glycosylasparaginase precursor D151N mutant

1P4K · N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase: “Crystal structure of the glycosylasparaginase precursor D151N mutant”. X-ray diffraction, 5 pockets (best druggability 0.58). MolNFT v1 #17802 on GenesisL1: 3D structure, binding…

PDB: 1P4K
Type: protein
Length: 590 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase
EC: 3.5.1.26
UniProt: Q47898
Pockets: 5 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase (EC 3.5.1.26)	protein	295	33% helix, 25% strand	Q47898

Ligands and binding sites

GOL · Glycerol · additive · 4 copies · chains A, C

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

Pockets

5 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	51	0.58	0.92	21	empty
2	147	0.48	0.78	21	empty
3	138	0.45	0.77	19	empty
4	73	0.41	0.79	13	empty
5	60	0.32	0.76	14	empty

Interfaces

1 interface between chains.

A–C · 2134 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

1P4K · Crystal structure of the glycosylasparaginase precursor D151N mutant · the same entry in another collection · chain A against A, TM-score 1.00
Q47898 · AlphaFold monomer V2.0 prediction for N(4)-(beta-N- acetylglucosaminyl)-L-asparaginase… · a predicted model of the same protein · chain C 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 Q47898
Elsewhere: RCSB PDB 1P4K · PDBe 1P4K · UniProt Q47898

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