MolNFT v1 · #124055 · protein

Wolinella succinogenes L-asparaginase P121 and L-aspartic acid

5K3O: “Wolinella succinogenes L-asparaginase P121 and L-aspartic acid”. X-ray diffraction, 1 ligand (ASP), 14 pockets (best druggability 0.72). MolNFT v1 #124055 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5K3O
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: ASP
Pockets: 14 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	L-asparaginase (EC 3.5.1.1)	protein	328	33% helix, 23% strand	P50286

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

14 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	877	0.72	0.77	73	empty
2	91	0.64	0.90	32	empty
3	97	0.59	0.87	27	empty
4	112	0.49	0.81	27	empty
5	104	0.48	0.81	26	empty

Interfaces

4 interfaces between chains.

A–B · 2363 Å² buried · 51 hydrogen bonds · protein-protein
C–D · 2357 Å² buried · 51 hydrogen bonds · protein-protein
B–C · 243 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 37 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5K3O · Wolinella succinogenes L-asparaginase P121 and L-Aspartic acid · the same entry in another collection · chain B against B, TM-score 1.00
P50286 · AlphaFold monomer V2.0 prediction for L-asparaginase (P50286) · 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 P50286
Elsewhere: RCSB PDB 5K3O · PDBe 5K3O · UniProt P50286

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