MolNFT v1 · #136740 · protein

Crystal structure of a mutant glycosylasparaginase (G172D) that causes the genetic disease aspartylglucosaminuria

5V2I: “Crystal structure of a mutant glycosylasparaginase (G172D) that causes the genetic disease…”. X-ray diffraction, 6 pockets (best druggability 0.51). MolNFT v1 #136740 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5V2I
Type: protein
Length: 550 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycosylasparaginase
UniProt: A0A1E3DWI1
Pockets: 6 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycosylasparaginase	protein	280	34% helix, 25% strand	A0A1E3DWI1
B	Glycosylasparaginase	protein	270	35% helix, 27% strand	A0A1E3DWI1

Pockets

6 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	57	0.51	0.87	25	empty
2	70	0.49	0.84	16	empty
3	192	0.46	0.75	36	empty
4	87	0.39	0.77	17	empty
5	99	0.37	0.75	22	empty

Interfaces

1 interface between chains.

A–B · 2020 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

5V2I · Crystal structure of a mutant glycosylasparaginase (G172D) that causes the genetic… · 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 A0A1E3DWI1
Elsewhere: RCSB PDB 5V2I · PDBe 5V2I · UniProt A0A1E3DWI1

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