Research workbench

Complex of mutant (K162M) of E. COLI L-asparaginase II with L-asp

Analyse Complex of mutant (K162M) of E. COLI L-asparaginase II with L-asp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6V26
Type: protein
Length: 1,284 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-asparaginase 2
EC: 3.5.1.1
UniProt: P00805
Ligands: ASP
Pockets: 13 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	L-asparaginase 2 (EC 3.5.1.1)	protein	326	33% helix, 23% strand	P00805
B	L-asparaginase 2 (EC 3.5.1.1)	protein	306	34% helix, 24% strand	P00805

Ligands and binding sites

ASP · Aspartic acid · ligand · 4 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	133	0.67	0.89	30	empty
2	135	0.64	0.87	31	empty
3	379	0.58	0.76	41	empty
4	70	0.53	0.86	27	ASP
5	120	0.51	0.81	31	ASP

Interfaces

3 interfaces between chains.

C–D · 2414 Å² buried · 53 hydrogen bonds · protein-protein
A–B · 2303 Å² buried · 45 hydrogen bonds · protein-protein
A–C · 314 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6V26 · Complex of mutant (K162M) of E. coli L-asparaginase II with L-Asp · 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 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 P00805
Elsewhere: RCSB PDB 6V26 · PDBe 6V26 · UniProt P00805

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