Research workbench
Crystal structure of alanyl-tRNA synthetase without oligomerization domain in lysine-methylated form
Analyse Crystal structure of alanyl-tRNA synthetase without oligomerization domain in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZZE
- Type
- protein
- Length
- 1,488 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
- O58035
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alanyl-tRNA synthetase (EC 6.1.1.7) | protein | 744 | 39% helix, 24% strand | O58035 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 828 | 0.75 | 0.79 | 69 | empty |
| 2 | 301 | 0.71 | 0.85 | 31 | empty |
| 3 | 507 | 0.68 | 0.79 | 57 | empty |
| 4 | 368 | 0.65 | 0.80 | 31 | empty |
| 5 | 310 | 0.65 | 0.80 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 121 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 82 modified (methylation, oxidation).
Compared structures
- 2ZZE · Crystal structure of alanyl-tRNA synthetase without oligomerization domain in… · the same entry in another collection · chain A against A, TM-score 1.00
- O58035 · AlphaFold monomer V2.0 prediction for alanine--tRNA ligase (O58035) · 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 O58035
- Elsewhere: RCSB PDB 2ZZE · PDBe 2ZZE · UniProt O58035
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