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Crystal structure of the E. COLI aspartyl-tRNA SYNTHETASE:YEAST TRNAASP:ASPARTYL-adenylate complex

Analyse Crystal structure of the E. COLI aspartyl-tRNA SYNTHETASE:YEAST… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1IL2
Type: protein + RNA
Length: 1,315 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aspartyl transfer RNA; Aspartyl-tRNA synthetase
EC: 6.1.1.12
UniProt: P21889
Ligands: AMO, SO4
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 34% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Aspartyl transfer RNA	rna	75	—	—
D	Aspartyl transfer RNA	rna	70	—	—
A, B	Aspartyl-tRNA synthetase (EC 6.1.1.12)	protein	585	34% helix, 27% strand	P21889

Ligands and binding sites

AMO · Aspartyl-adenosine-5'-monophosphate · ligand · 2 copies · chains C, A, B
SO4 · Sulfate ion · ion · 2 copies · chains C, A, 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, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1015	0.83	0.84	105	SO4, AMO
2	186	0.82	0.96	44	empty
3	929	0.72	0.78	43	empty
4	661	0.72	0.80	54	empty
5	600	0.71	0.80	37	empty

Interfaces

4 interfaces between chains.

A–B · 5190 Å² buried · 81 hydrogen bonds · protein-protein
C–A · 2162 Å² buried · 75 hydrogen bonds · protein-nucleic
D–B · 1260 Å² buried · 47 hydrogen bonds · protein-nucleic
C–B · 28 Å² buried · 0 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

1IL2 · Crystal Structure of the E. coli Aspartyl-tRNA Synthetase:Yeast… · the same entry in another collection · chain C against C, TM-score 1.00
P21889 · AlphaFold monomer V2.0 prediction for aspartate--tRNA ligase (P21889) · a predicted model of the same protein · chain B 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 P21889
Elsewhere: RCSB PDB 1IL2 · PDBe 1IL2 · UniProt P21889

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