Research workbench

Erwinia chrysanthemi L-asparaginase + aspartic acid

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

PDB: 5F52
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: 11 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	L-asparaginase (EC 3.5.1.1)	protein	324	32% helix, 23% strand	P06608

Ligands and binding sites

ASP · Aspartic acid · ligand · 4 copies · chains A, C, B, D
PEG · Di(hydroxyethyl)ether · additive · 5 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, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	393	0.83	0.92	52	empty
2	382	0.79	0.88	51	PEG, ASP
3	387	0.78	0.88	50	ASP
4	385	0.78	0.88	52	ASP
5	407	0.78	0.87	50	ASP

Interfaces

6 interfaces between chains.

A–C · 2389 Å² buried · 43 hydrogen bonds · protein-protein
B–D · 2365 Å² buried · 43 hydrogen bonds · protein-protein
B–C · 1112 Å² buried · 23 hydrogen bonds · protein-protein
A–D · 1111 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1030 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

5F52 · Erwinia chrysanthemi L-asparaginase + Aspartic acid · the same entry in another collection · chain C against C, TM-score 1.00
P06608 · AlphaFold monomer V2.0 prediction for L-asparaginase (P06608) · 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 P06608
Elsewhere: RCSB PDB 5F52 · PDBe 5F52 · UniProt P06608

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