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Asparaginase from E. COLI, mutant T89V with covalently bound aspartate

Analyse Asparaginase from E. COLI, mutant T89V with covalently bound aspartate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ECA
Type: protein
Length: 1,304 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-asparagine amidohydrolase
EC: 3.5.1.1
UniProt: P00805
Pockets: 11 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	L-asparagine amidohydrolase (EC 3.5.1.1)	protein	326	34% helix, 24% strand	P00805

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	215	0.81	0.95	54	empty
2	194	0.79	0.94	52	empty
3	164	0.78	0.95	43	empty
4	120	0.77	0.96	29	empty
5	80	0.71	0.95	30	empty

Interfaces

6 interfaces between chains.

A–C · 2408 Å² buried · 56 hydrogen bonds · protein-protein
B–D · 2407 Å² buried · 55 hydrogen bonds · protein-protein
A–D · 1057 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 1039 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1029 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 4 modified (disulfide, nonstandard).

Compared structures

4ECA · Asparaginase from E. COLI, mutant T89V with covalently bound aspartate · the same entry in another collection · chain D against D, 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 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 P00805
Elsewhere: RCSB PDB 4ECA · PDBe 4ECA · UniProt P00805

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