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A subcomplex crystal structure of human cytosolic aspartyl-tRNA synthetase and heterotetrameric glutathione transferase-homology domains in multi-tRNA synthetase complex

Analyse A subcomplex crystal structure of human cytosolic aspartyl-tRNA synthetase and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Y6L
Type: protein
Length: 825 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methionine--tRNA ligase, cytoplasmic; Eukaryotic translation elongation factor 1…
EC: 6.1.1.10, 6.1.1.17, 6.1.1.12
UniProt: P56192, O43324, P07814, Q13155, P14868
Ligands: PO4
Pockets: 12 · best druggability 0.76

Structure

x-ray diffraction · 5 distinct chains · 51% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methionine--tRNA ligase, cytoplasmic (EC 6.1.1.10)	protein	211	55% helix, 6% strand	P56192
B	Eukaryotic translation elongation factor 1 epsilon-1	protein	173	54% helix, 5% strand	O43324
C	Bifunctional GLUTAMATE/PROLINE--tRNA ligase (EC 6.1.1.17)	protein	170	52% helix, 11% strand	P07814
D	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2	protein	213	46% helix, 14% strand	Q13155
E	Aspartate--tRNA ligase, cytoplasmic (EC 6.1.1.12)	protein	58	43% helix, 14% strand	P14868

Ligands and binding sites

PO4 · Phosphate ion · ion · 2 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1086	0.76	0.78	91	empty
2	207	0.65	0.84	37	empty
3	277	0.62	0.80	33	empty
4	331	0.59	0.77	34	empty
5	258	0.56	0.78	43	empty

Interfaces

6 interfaces between chains.

A–B · 1244 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1142 Å² buried · 10 hydrogen bonds · protein-protein
D–E · 978 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 787 Å² buried · 2 hydrogen bonds · protein-protein
B–E · 309 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5Y6L · A subcomplex crystal structure of human cytosolic aspartyl-tRNA synthetase and… · the same entry in another collection · chain E against E, TM-score 1.00
P07814 · AlphaFold monomer V2.0 prediction for bifunctional GLUTAMATE/PROLINE --tRNA ligase… · a predicted model of the same protein · chain C against A, TM-score 0.97
P56192 · AlphaFold monomer V2.0 prediction for methionine--tRNA ligase, cytoplasmic (P56192) · a predicted model of the same protein · chain A against A, TM-score 0.96
P14868 · AlphaFold monomer V2.0 prediction for aspartate--tRNA ligase, cytoplasmic (P14868) · a predicted model of the same protein · chain E against A, TM-score 0.96
O43324 · AlphaFold monomer V2.0 prediction for eukaryotic translation elongation factor 1… · a predicted model of the same protein · chain B against A, TM-score 0.96
Q13155 · AlphaFold monomer V2.0 prediction for aminoacyl tRNA synthase complex-interacting… · a predicted model of the same protein · chain D against A, TM-score 0.94

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 P56192
Every structure of UniProt O43324
Every structure of UniProt P07814
Every structure of UniProt Q13155
Every structure of UniProt P14868
Elsewhere: RCSB PDB 5Y6L · PDBe 5Y6L · UniProt P56192 · UniProt O43324 · UniProt P07814 · UniProt Q13155 · UniProt P14868

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