Research workbench
Crystal structure of the E. COLI aspartyl-tRNA synthetase : trnaasp : aspartyl-adenylate complex
Analyse Crystal structure of the E. COLI aspartyl-tRNA synthetase : trnaasp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1C0A
- Type
- protein + RNA
- Length
- 662 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartyl tRNA; Aspartyl tRNA synthetase
- EC
- 6.1.1.12
- UniProt
- P21889
- Ligands
- AMP, AMO, SO4
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Aspartyl tRNA | rna | 77 | — | — |
| A | Aspartyl tRNA synthetase (EC 6.1.1.12) | protein | 585 | 34% helix, 25% strand | P21889 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- AMO · Aspartyl-adenosine-5'-monophosphate · ligand · chains B, A
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1118 | 0.81 | 0.82 | 84 | AMO |
| 2 | 670 | 0.74 | 0.81 | 50 | empty |
| 3 | 826 | 0.68 | 0.76 | 45 | SO4 |
| 4 | 57 | 0.52 | 0.87 | 16 | empty |
| 5 | 226 | 0.51 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- B–A · 2307 Ų buried · 69 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 9 modified (nucleotide modification).
Compared structures
- 1C0A · Crystal structure of the E. COLI aspartyl-tRNA synthetase : trnaasp : aspartyl-adenylate… · the same entry in another collection · chain B against B, TM-score 1.00
- P21889 · AlphaFold monomer V2.0 prediction for aspartate--tRNA ligase (P21889) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P21889
- Elsewhere: RCSB PDB 1C0A · PDBe 1C0A · UniProt P21889
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