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Crystal structure of pyrococcus horikoshii arginyl-tRNA synthetase complexed with TRNA(ARG) and an ATP analog (anp)
Analyse Crystal structure of pyrococcus horikoshii arginyl-tRNA synthetase complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZUE
- Type
- protein + RNA
- Length
- 704 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginyl-tRNA synthetase; TRNA-arg
- EC
- 6.1.1.19
- UniProt
- O59147
- Ligands
- ANP, MG
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginyl-tRNA synthetase (EC 6.1.1.19) | protein | 628 | 54% helix, 12% strand | O59147 |
| B | TRNA-arg | rna | 76 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 734 | 0.78 | 0.83 | 68 | empty |
| 2 | 525 | 0.75 | 0.83 | 70 | ANP |
| 3 | 312 | 0.63 | 0.80 | 41 | empty |
| 4 | 85 | 0.61 | 0.89 | 19 | empty |
| 5 | 263 | 0.60 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2579 Ų buried · 41 hydrogen bonds · protein-nucleic
Compared structures
- 2ZUE · Crystal structure of Pyrococcus horikoshii arginyl-tRNA synthetase complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- O59147 · AlphaFold monomer V2.0 prediction for arginine--tRNA ligase (O59147) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 O59147
- Elsewhere: RCSB PDB 2ZUE · PDBe 2ZUE · UniProt O59147
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