Research workbench

Wolinella succinogenes L-asparaginase P121 + L-glutamic acid

Analyse Wolinella succinogenes L-asparaginase P121 + L-glutamic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5K45
Type: protein
Length: 1,312 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-asparaginase
EC: 3.5.1.1
UniProt: P50286
Ligands: GLU
Pockets: 11 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	L-asparaginase (EC 3.5.1.1)	protein	328	33% helix, 20% strand	P50286

Ligands and binding sites

GLU · Glutamic 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

11 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	879	0.73	0.77	74	empty
2	135	0.66	0.88	36	empty
3	105	0.60	0.87	31	empty
4	191	0.51	0.77	27	GLU
5	205	0.50	0.76	27	GLU

Interfaces

4 interfaces between chains.

A–B · 2055 Å² buried · 43 hydrogen bonds · protein-protein
C–D · 2046 Å² buried · 43 hydrogen bonds · protein-protein
B–C · 264 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 39 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5K45 · Wolinella succinogenes L-asparaginase P121 + L-Glutamic acid · the same entry in another collection · chain D against D, TM-score 1.00
P50286 · AlphaFold monomer V2.0 prediction for L-asparaginase (P50286) · a predicted model of the same protein · chain B against A, TM-score 0.95

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 P50286
Elsewhere: RCSB PDB 5K45 · PDBe 5K45 · UniProt P50286

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