Research workbench
Crystal structure of aspartyl-tRNA synthetase from thermus thermophilus complexed to trnaasp from escherichia COLI
Analyse Crystal structure of aspartyl-tRNA synthetase from thermus thermophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EFW
- Type
- protein + RNA
- Length
- 1,306 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartyl-tRNA; Aspartyl-tRNA synthetase
- EC
- 6.1.1.12
- UniProt
- P36419
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | Aspartyl-tRNA | rna | 73 | — | — |
| A, B | Aspartyl-tRNA synthetase (EC 6.1.1.12) | protein | 580 | 32% helix, 25% strand | P36419 |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.82 | 0.97 | 26 | empty |
| 2 | 849 | 0.76 | 0.80 | 57 | empty |
| 3 | 853 | 0.76 | 0.80 | 59 | empty |
| 4 | 840 | 0.76 | 0.79 | 74 | empty |
| 5 | 774 | 0.75 | 0.80 | 76 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5739 Ų buried · 96 hydrogen bonds · protein-protein
- C–A · 1268 Ų buried · 39 hydrogen bonds · protein-nucleic
- D–B · 1038 Ų buried · 35 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 20 modified (nucleotide modification).
Compared structures
- 1EFW · Crystal structure of aspartyl-tRNA synthetase from Thermus thermophilus complexed to… · the same entry in another collection · chain C against C, TM-score 1.00
- P36419 · AlphaFold monomer V2.0 prediction for aspartate--TRNA(ASP) ligase (P36419) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P36419
- Elsewhere: RCSB PDB 1EFW · PDBe 1EFW · UniProt P36419
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