Research workbench
Histidyl-tRNA synthetase
Analyse Histidyl-tRNA synthetase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HTT
- Type
- protein
- Length
- 1,446 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidyl-tRNA synthetase
- EC
- 6.1.1.21
- UniProt
- P04804
- Ligands
- HIS, AMP
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 366 | 40% helix, 24% strand | P04804 |
| B, D | Histidyl-tRNA synthetase (EC 6.1.1.21) | protein | 357 | 39% helix, 26% strand | P04804 |
Ligands and binding sites
- HIS · Histidine · ligand · 4 copies · chains A, B, C, D
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.80 | 0.82 | 106 | empty |
| 2 | 890 | 0.80 | 0.82 | 97 | empty |
| 3 | 1024 | 0.78 | 0.80 | 76 | empty |
| 4 | 245 | 0.71 | 0.87 | 38 | HIS, AMP |
| 5 | 245 | 0.70 | 0.86 | 39 | HIS, AMP |
Interfaces
6 interfaces between chains.
- A–B · 3955 Ų buried · 60 hydrogen bonds · protein-protein
- C–D · 3955 Ų buried · 65 hydrogen bonds · protein-protein
- B–C · 186 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 146 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 38 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1HTT · Histidyl-tRNA synthetase · the same entry in another collection · chain B against B, TM-score 1.00
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 P04804
- Elsewhere: RCSB PDB 1HTT · PDBe 1HTT · UniProt P04804
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