Research workbench
Crystal structure of aquifex aeolicus methionyl-tRNA synthetase complexed with TRNA(MET) and methionyl-adenylate anologue
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
- 2CT8
- Type
- protein + RNA
- Length
- 1,078 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (74-mer); Methionyl-tRNA synthetase
- EC
- 6.1.1.10
- UniProt
- O67298
- Ligands
- MSP
- Pockets
- 18 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | RNA (74-mer) | rna | 74 | — | — |
| A, B | Methionyl-tRNA synthetase (EC 6.1.1.10) | protein | 465 | 52% helix, 13% strand | O67298 |
Ligands and binding sites
- MSP · 5'-O-[(L-methionyl)-sulphamoyl]adenosine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.76 | 0.79 | 87 | empty |
| 2 | 924 | 0.74 | 0.79 | 77 | empty |
| 3 | 1122 | 0.71 | 0.76 | 71 | empty |
| 4 | 262 | 0.65 | 0.82 | 33 | MSP |
| 5 | 577 | 0.65 | 0.77 | 24 | empty |
Interfaces
4 interfaces between chains.
- D–B · 1206 Ų buried · 29 hydrogen bonds · protein-nucleic
- C–A · 1119 Ų buried · 31 hydrogen bonds · protein-nucleic
- A–B · 936 Ų buried · 16 hydrogen bonds · protein-protein
- D–A · 12 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 2CT8 · 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 2CT8 · PDBe 2CT8 · UniProt O67298
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