MolNFT v1 · #28489 · protein
Crystal structure of alanyl-tRNA synthetase in complex with ATP and magnesium
1YFR: “Crystal structure of alanyl-tRNA synthetase in complex with ATP and magnesium”. X-ray diffraction, 2 ligands (ATP, MG), 11 pockets (best druggability 0.65). MolNFT v1 #28489 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1YFR
- Type
- protein
- Length
- 896 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanyl-tRNA synthetase
- EC
- 6.1.1.7
- UniProt
- O67323
- Ligands
- ATP, MG
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alanyl-tRNA synthetase (EC 6.1.1.7) | protein | 448 | 44% helix, 19% strand | O67323 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.65 | 0.78 | 42 | MG, ATP |
| 2 | 444 | 0.65 | 0.78 | 52 | MG, ATP |
| 3 | 182 | 0.52 | 0.78 | 29 | empty |
| 4 | 110 | 0.46 | 0.79 | 26 | empty |
| 5 | 64 | 0.45 | 0.82 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 35 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1YFR · crystal structure of alanyl-tRNA synthetase in complex with ATP and magnesium · the same entry in another collection · chain A against A, TM-score 1.00
- O67323 · AlphaFold monomer V2.0 prediction for alanine--tRNA ligase (O67323) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 O67323
- Elsewhere: RCSB PDB 1YFR · PDBe 1YFR · UniProt O67323
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