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Crystal structure of alanyl-tRNA synthetase in complex with 5''-O-(N-(L-alanyl)-sulfamyoxyl) adenine without oligomerization domain
Analyse Crystal structure of alanyl-tRNA synthetase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZZG
- Type
- protein
- Length
- 1,475 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.1
- Source
- Pyrococcus horikoshii
- Molecule
- Alanyl-tRNA synthetase
- EC
- 6.1.1.7
- UniProt
- O58035
- Ligands
- A5A, ZN
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · resolution 3.1 · 2 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanyl-tRNA synthetase (EC 6.1.1.7) | protein | 738 | 37% helix, 23% strand | O58035 |
| B | Alanyl-tRNA synthetase (EC 6.1.1.7) | protein | 737 | 36% helix, 22% strand | O58035 |
Ligands and binding sites
- A5A · 5'-O-(N-(L-alanyl)-sulfamoyl)adenosine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 802 | 0.76 | 0.80 | 79 | A5A |
| 2 | 707 | 0.73 | 0.79 | 66 | A5A |
| 3 | 70 | 0.71 | 0.96 | 21 | empty |
| 4 | 348 | 0.69 | 0.82 | 33 | empty |
| 5 | 284 | 0.68 | 0.83 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 702 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
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 2ZZG · PDBe 2ZZG · UniProt O58035
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