Research workbench
Human cytosolic Histidyl-tRNA synthetase (HisRS) with WHEP domain
Analyse Human cytosolic Histidyl-tRNA synthetase (HisRS) with WHEP domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O76
- Type
- protein
- Length
- 889 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.787
- Source
- Homo sapiens
- Molecule
- Histidine--tRNA ligase, cytoplasmic
- EC
- 6.1.1.21
- UniProt
- P12081
- Ligands
- CL
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.787 · 2 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidine--tRNA ligase, cytoplasmic (EC 6.1.1.21) | protein | 438 | 44% helix, 21% strand | P12081 |
| B | Histidine--tRNA ligase, cytoplasmic (EC 6.1.1.21) | protein | 451 | 49% helix, 19% strand | P12081 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.82 | 0.86 | 43 | empty |
| 2 | 711 | 0.70 | 0.77 | 66 | empty |
| 3 | 627 | 0.67 | 0.76 | 74 | empty |
| 4 | 687 | 0.67 | 0.76 | 63 | empty |
| 5 | 58 | 0.64 | 0.94 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 4130 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 6O76 · Human cytosolic histidyl-tRNA synthetase (hisrs) with whep domain · the same entry in another collection · chain A against A, TM-score 1.00
- P12081 · AlphaFold monomer V2.0 prediction for histidine--tRNA ligase, cytoplasmic (P12081) · a predicted model of the same protein · chain A 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 P12081
- Elsewhere: RCSB PDB 6O76 · PDBe 6O76 · UniProt P12081
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