MolNFT v1 · #1158 · protein + RNA

The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction

1ASZ · T-RNA (75-mer): “The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation…”. X-ray diffraction, 1 ligand (ATP), 20 pockets (best druggability 0.82). MolNFT v1 #1158 on GenesisL1: 3D…

PDB: 1ASZ
Type: protein + RNA
Length: 1,130 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: T-RNA (75-mer); Aspartyl-tRNA synthetase
EC: 6.1.1.12
UniProt: P04802
Ligands: ATP
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
R, S	T-RNA (75-mer) (EC 6.1.1.12)	rna	75	—	—
A, B	Aspartyl-tRNA synthetase	protein	490	30% helix, 24% strand	P04802

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains R, A, S, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	475	0.82	0.89	62	ATP
2	525	0.80	0.87	58	ATP
3	1038	0.80	0.82	71	empty
4	742	0.79	0.84	50	empty
5	1053	0.78	0.80	77	empty

Interfaces

4 interfaces between chains.

A–B · 4688 Å² buried · 90 hydrogen bonds · protein-protein
S–B · 2173 Å² buried · 68 hydrogen bonds · protein-nucleic
R–A · 2141 Å² buried · 53 hydrogen bonds · protein-nucleic
S–A · 30 Å² buried · 1 hydrogen bond · protein-nucleic

Modifications

Observed in the structure: 16 modified (nucleotide modification).

Compared structures

1ASZ · The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of… · the same entry in another collection · chain R against R, TM-score 1.00
P04802 · AlphaFold monomer V2.0 prediction for aspartate--tRNA ligase, cytoplasmic (P04802) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P04802
Elsewhere: RCSB PDB 1ASZ · PDBe 1ASZ · UniProt P04802

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