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Crystal structure of the archaeal asparagine synthetase a complexed with L-asparagine

Analyse Crystal structure of the archaeal asparagine synthetase a complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3P8Y
Type: protein
Length: 588 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Asns-like asparaginyl-tRNA synthetase related protein
UniProt: Q9V228
Ligands: ASN
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Asns-like asparaginyl-tRNA synthetase related protein	protein	294	37% helix, 23% strand	Q9V228

Ligands and binding sites

ASN · Asparagine · ligand · 2 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	188	0.79	0.95	40	ASN
2	237	0.79	0.92	50	ASN
3	80	0.39	0.78	16	empty
4	59	0.35	0.77	13	empty
5	70	0.34	0.76	13	empty

Interfaces

1 interface between chains.

A–B · 2927 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

3P8Y · Crystal structure of the archaeal asparagine synthetase A complexed with L-Asparagine · the same entry in another collection · chain A 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 Q9V228
Elsewhere: RCSB PDB 3P8Y · PDBe 3P8Y · UniProt Q9V228

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