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Crystal structure of argininosuccinate synthase from legionella pneumophila philadelphia 1

Analyse Crystal structure of argininosuccinate synthase from legionella pneumophila… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XNQ
Type: protein
Length: 1,556 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Argininosuccinate synthase
EC: 6.3.4.5
UniProt: Q5ZY78
Ligands: SO4
Pockets: 13 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Argininosuccinate synthase (EC 6.3.4.5)	protein	389	44% helix, 20% strand	Q5ZY78

Ligands and binding sites

SO4 · Sulfate ion · ion · 7 copies · chains A, C, D, B
EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	664	0.86	0.90	75	SO4
2	414	0.84	0.92	67	SO4
3	524	0.83	0.89	78	empty
4	700	0.73	0.79	55	SO4, EDO
5	676	0.73	0.79	54	EDO

Interfaces

6 interfaces between chains.

C–D · 3708 Å² buried · 47 hydrogen bonds · protein-protein
A–B · 3697 Å² buried · 43 hydrogen bonds · protein-protein
B–C · 1001 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 985 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 879 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6XNQ · Crystal Structure of Argininosuccinate synthase from Legionella pneumophila Philadelphia 1 · the same entry in another collection · chain D against D, TM-score 1.00
Q5ZY78 · AlphaFold monomer V2.0 prediction for argininosuccinate synthase (Q5ZY78) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q5ZY78
Elsewhere: RCSB PDB 6XNQ · PDBe 6XNQ · UniProt Q5ZY78

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