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Crystal structure of erwinia chrysanthemi L-asparaginase complexed with 6-hydroxy-D-norleucine

Analyse Crystal structure of erwinia chrysanthemi L-asparaginase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1JSL
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: DDO
Pockets: 11 · best druggability 0.78

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

DDO · 6-hydroxy-D-norleucine · ligand · 4 copies · chains A, C, B, D
GOL · Glycerol · additive · 3 copies · chains C, D
1PE · Pentaethylene glycol · additive · chains A

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

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	189	0.78	0.94	29	empty
2	232	0.75	0.89	48	DDO
3	279	0.74	0.87	50	DDO
4	219	0.74	0.89	42	DDO
5	235	0.73	0.88	48	DDO

Interfaces

6 interfaces between chains.

B–D · 2435 Å² buried · 47 hydrogen bonds · protein-protein
A–C · 2415 Å² buried · 46 hydrogen bonds · protein-protein
A–B · 1145 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 1140 Å² buried · 27 hydrogen bonds · protein-protein
B–C · 1127 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 covalent (covalent ligand).

Compared structures

1JSL · Crystal structure of Erwinia chrysanthemi L-asparaginase complexed with… · 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 B 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 1JSL · PDBe 1JSL · UniProt P06608

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