MolNFT v1 · #16724 · protein

Atomic resolution structure of erwinia chrysanthemi L-asparaginase

1O7J: “Atomic resolution structure of erwinia chrysanthemi L-asparaginase”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.78). MolNFT v1 #16724 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1O7J
Type: protein
Length: 1,300 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: SO4
Pockets: 12 · best druggability 0.78

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	325	32% helix, 23% strand	P06608

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, D
GOL · Glycerol · additive · 2 copies · chains A, C, D

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

Pockets

12 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	195	0.78	0.93	31	GOL
2	291	0.76	0.88	51	SO4
3	265	0.75	0.88	46	SO4
4	253	0.75	0.88	46	SO4
5	293	0.74	0.87	50	SO4

Interfaces

6 interfaces between chains.

A–C · 2431 Å² buried · 43 hydrogen bonds · protein-protein
B–D · 2407 Å² buried · 45 hydrogen bonds · protein-protein
C–D · 1138 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 1135 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 1129 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

1O7J · Atomic resolution structure of Erwinia chrysanthemi L-asparaginase · 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 1O7J · PDBe 1O7J · UniProt P06608

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