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Structure of histidinyl-tRNA synthetase in complex with TRNA(HIS)

Analyse Structure of histidinyl-tRNA synthetase in complex with TRNA(HIS) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4RDX
Type: protein + RNA
Length: 486 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histidine--tRNA ligase; TRNA(HIS)
EC: 6.1.1.21
UniProt: P62374
Ligands: AMP, HIS
Pockets: 7 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histidine--tRNA ligase (EC 6.1.1.21)	protein	409	42% helix, 23% strand	P62374
C	TRNA(HIS)	rna	77	—	—

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · chains A, C
HIS · Histidine · ligand · chains A, C

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	555	0.79	0.86	62	AMP, HIS
2	690	0.65	0.76	39	empty
3	589	0.65	0.77	34	empty
4	157	0.45	0.76	32	empty
5	109	0.38	0.75	22	empty

Interfaces

1 interface between chains.

A–C · 1869 Å² buried · 53 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

4RDX · Structure of histidinyl-tRNA synthetase in complex with tRNA(His) · the same entry in another collection · chain A against A, TM-score 1.00
P62374 · AlphaFold monomer V2.0 prediction for histidine--tRNA ligase (P62374) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P62374
Elsewhere: RCSB PDB 4RDX · PDBe 4RDX · UniProt P62374

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