Research workbench
Crystal structure of histidyl-tRNA synthetase from nostoc sp. pcc 7120
Analyse Crystal structure of histidyl-tRNA synthetase from nostoc sp. pcc 7120 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NET
- Type
- protein
- Length
- 846 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidyl-tRNA synthetase
- EC
- 6.1.1.21
- UniProt
- Q8YMC2
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 431 | 46% helix, 20% strand | Q8YMC2 |
| B | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 415 | 40% helix, 21% strand | Q8YMC2 |
Ligands and binding sites
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.86 | 0.95 | 40 | empty |
| 2 | 191 | 0.69 | 0.87 | 35 | empty |
| 3 | 258 | 0.69 | 0.84 | 46 | empty |
| 4 | 384 | 0.59 | 0.76 | 45 | empty |
| 5 | 68 | 0.58 | 0.89 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 4096 Ų buried · 61 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3NET · Crystal structure of histidyl-tRNA synthetase from Nostoc sp. PCC 7120 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8YMC2 · AlphaFold monomer V2.0 prediction for histidine--tRNA ligase (Q8YMC2) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q8YMC2
- Elsewhere: RCSB PDB 3NET · PDBe 3NET · UniProt Q8YMC2
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