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Crystal structure of L-asparaginase I from yersinia pestis

Analyse Crystal structure of L-asparaginase I from yersinia pestis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3NTX
Type: protein
Length: 662 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytoplasmic L-asparaginase I
EC: 3.5.1.1
UniProt: Q7CIH5
Pockets: 8 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cytoplasmic L-asparaginase I (EC 3.5.1.1)	protein	331	31% helix, 22% strand	Q7CIH5

Ligands and binding sites

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

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	328	0.62	0.79	45	empty
2	60	0.54	0.88	18	empty
3	61	0.53	0.88	17	empty
4	63	0.39	0.80	16	empty
5	63	0.39	0.80	16	GOL

Interfaces

1 interface between chains.

A–B · 494 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 modified (engineered).

Compared structures

3NTX · Crystal Structure of L-asparaginase I from Yersinia pestis · 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 Q7CIH5
Elsewhere: RCSB PDB 3NTX · PDBe 3NTX · UniProt Q7CIH5

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