Research workbench
Crystal structure of aquifex aeolicus methionyl-tRNA synthetase complexed with TRNA(MET)
Analyse Crystal structure of aquifex aeolicus methionyl-tRNA synthetase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CSX
- Type
- protein + RNA
- Length
- 1,078 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (75-mer); Methionyl-tRNA synthetase
- EC
- 6.1.1.10
- UniProt
- O67298
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | RNA (75-mer) | rna | 75 | — | — |
| A, B | Methionyl-tRNA synthetase (EC 6.1.1.10) | protein | 464 | 51% helix, 14% strand | O67298 |
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.77 | 0.79 | 94 | empty |
| 2 | 887 | 0.76 | 0.80 | 64 | empty |
| 3 | 815 | 0.74 | 0.78 | 73 | empty |
| 4 | 833 | 0.72 | 0.78 | 60 | empty |
| 5 | 444 | 0.66 | 0.78 | 43 | empty |
Interfaces
4 interfaces between chains.
- D–B · 1195 Ų buried · 38 hydrogen bonds · protein-nucleic
- C–A · 1165 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–B · 872 Ų buried · 10 hydrogen bonds · protein-protein
- D–A · 18 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 2CSX · Crystal structure of Aquifex aeolicus methionyl-tRNA synthetase complexed with tRNA(Met) · the same entry in another collection · chain C against C, TM-score 1.00
- O67298 · AlphaFold monomer V2.0 prediction for methionine--tRNA ligase (O67298) · a predicted model of the same protein · chain A 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 O67298
- Elsewhere: RCSB PDB 2CSX · PDBe 2CSX · UniProt O67298
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.