MolNFT v1 · #121737 · protein

Erwinia chrysanthemi L-asparaginase A31I + E63Q mutation + aspartic acid

5I48: “Erwinia chrysanthemi L-asparaginase A31I + E63Q mutation + aspartic acid”. X-ray diffraction, 1 ligand (ASP), 10 pockets (best druggability 0.87). MolNFT v1 #121737 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5I48
Type: protein
Length: 1,296 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-asparaginase
EC: 3.5.1.1
UniProt: P06608
Ligands: ASP
Pockets: 10 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	L-asparaginase (EC 3.5.1.1)	protein	324	32% helix, 24% strand	P06608

Ligands and binding sites

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

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

Pockets

10 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	530	0.87	0.93	89	empty
2	421	0.78	0.87	52	ASP
3	348	0.77	0.87	48	ASP
4	336	0.77	0.88	49	ASP
5	348	0.77	0.87	52	ASP

Interfaces

6 interfaces between chains.

A–C · 2397 Å² buried · 44 hydrogen bonds · protein-protein
B–D · 2364 Å² buried · 44 hydrogen bonds · protein-protein
A–D · 1114 Å² buried · 24 hydrogen bonds · protein-protein
B–C · 1106 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1051 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

5I48 · Erwinia chrysanthemi L-asparaginase A31I + E63Q mutation + Aspartic acid · the same entry in another collection · chain D against D, TM-score 1.00
P06608 · AlphaFold monomer V2.0 prediction for L-asparaginase (P06608) · 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 P06608
Elsewhere: RCSB PDB 5I48 · PDBe 5I48 · UniProt P06608

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