Research workbench

Erwinia chrysanthemi L-asparaginase + glutamic acid

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

PDB: 5HW0
Type: protein
Length: 1,255 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: GLU
Pockets: 14 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	L-asparaginase (EC 3.5.1.1)	protein	311	33% helix, 22% strand	P06608
B	L-asparaginase (EC 3.5.1.1)	protein	308	33% helix, 24% strand	P06608
D	L-asparaginase (EC 3.5.1.1)	protein	325	32% helix, 23% strand	P06608

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

14 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	523	0.86	0.93	85	empty
2	99	0.74	0.96	31	empty
3	274	0.73	0.87	49	GLU
4	464	0.64	0.77	43	GLU
5	435	0.63	0.77	47	GLU

Interfaces

6 interfaces between chains.

C–D · 2305 Å² buried · 44 hydrogen bonds · protein-protein
A–B · 2210 Å² buried · 42 hydrogen bonds · protein-protein
A–C · 1114 Å² buried · 27 hydrogen bonds · protein-protein
B–D · 1107 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 934 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

5HW0 · Erwinia chrysanthemi L-asparaginase + Glutamic 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 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 5HW0 · PDBe 5HW0 · UniProt P06608

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