Research workbench
Crystal structure of a histidyl-tRNA synthetase hisrs from burkholderia thailandensis bound to histidine
Analyse Crystal structure of a histidyl-tRNA synthetase hisrs from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E51
- Type
- protein
- Length
- 812 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidine--tRNA ligase
- EC
- 6.1.1.21
- UniProt
- Q2SWE3
- Ligands
- HIS
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidine--tRNA ligase (EC 6.1.1.21) | protein | 415 | 43% helix, 21% strand | Q2SWE3 |
| B | Histidine--tRNA ligase (EC 6.1.1.21) | protein | 397 | 41% helix, 22% strand | Q2SWE3 |
Ligands and binding sites
- HIS · Histidine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.82 | 0.83 | 114 | empty |
| 2 | 579 | 0.68 | 0.78 | 62 | HIS |
| 3 | 452 | 0.64 | 0.78 | 48 | HIS |
| 4 | 241 | 0.60 | 0.80 | 38 | empty |
| 5 | 144 | 0.50 | 0.79 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 4051 Ų buried · 61 hydrogen bonds · protein-protein
Compared structures
- 4E51 · Crystal structure of a histidyl-tRNA synthetase HisRS from Burkholderia thailandensis… · the same entry in another collection · chain B against B, TM-score 1.00
- Q2SWE3 · AlphaFold monomer V2.0 prediction for histidine--tRNA ligase (Q2SWE3) · 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 Q2SWE3
- Elsewhere: RCSB PDB 4E51 · PDBe 4E51 · UniProt Q2SWE3
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