Research workbench
Crystal structure of alanyl-tRNA synthetase from pyrococcus horikoshii OT3
Analyse Crystal structure of alanyl-tRNA synthetase from pyrococcus horikoshii OT3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V4P
- Type
- protein
- Length
- 457 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanyl-tRNA synthetase
- EC
- 6.1.1.7
- UniProt
- O58307
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alanyl-tRNA synthetase (EC 6.1.1.7) | protein | 151 | 36% helix, 33% strand | O58307 |
| C | Alanyl-tRNA synthetase (EC 6.1.1.7) | protein | 155 | 36% helix, 32% strand | O58307 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.66 | 0.80 | 34 | empty |
| 2 | 260 | 0.62 | 0.80 | 38 | empty |
| 3 | 268 | 0.60 | 0.79 | 23 | empty |
| 4 | 239 | 0.58 | 0.79 | 35 | empty |
| 5 | 162 | 0.49 | 0.77 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–C · 607 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 535 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1V4P · Crystal structure of Alanyl-tRNA Synthetase from Pyrococcus horikoshii OT3 · the same entry in another collection · chain A against A, TM-score 1.00
- O58307 · AlphaFold monomer V2.0 prediction for alanyl-tRNA editing protein alax-S (O58307) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O58307
- Elsewhere: RCSB PDB 1V4P · PDBe 1V4P · UniProt O58307
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