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Crystal structure analysis of E. COLI L-asparaginase II (Y25F mutant)

Analyse Crystal structure analysis of E. COLI L-asparaginase II (Y25F mutant) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1HO3
Type: protein
Length: 652 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-asparaginase II
EC: 3.5.1.1
UniProt: P00805
Ligands: ASP
Pockets: 7 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	L-asparaginase II (EC 3.5.1.1)	protein	326	32% helix, 22% strand	P00805

Ligands and binding sites

ASP · Aspartic acid · ligand · 2 copies · chains A, B

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

Pockets

7 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	307	0.64	0.81	39	ASP
2	322	0.63	0.79	40	ASP
3	175	0.50	0.77	43	empty
4	90	0.43	0.79	28	empty
5	76	0.38	0.78	19	empty

Interfaces

1 interface between chains.

A–B · 919 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

1HO3 · Crystal structure analysis of E. COLI L-asparaginase II (Y25F mutant) · the same entry in another collection · chain A against A, TM-score 1.00
P00805 · AlphaFold monomer V2.0 prediction for L-asparaginase 2 (P00805) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P00805
Elsewhere: RCSB PDB 1HO3 · PDBe 1HO3 · UniProt P00805

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