MolNFT v1 · #26716 · protein
Structure of archaeal trans-editing protein alax in complex with zinc
1WXO · Alanyl-tRNA synthetase: “Structure of archaeal trans-editing protein alax in complex with zinc”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.68). MolNFT v1 #26716 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1WXO
- Type
- protein
- Length
- 458 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanyl-tRNA synthetase
- UniProt
- O58307
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Alanyl-tRNA synthetase | protein | 152 | 36% helix, 33% strand | O58307 |
| B | Alanyl-tRNA synthetase | protein | 154 | 36% helix, 32% strand | O58307 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 422 | 0.68 | 0.80 | 48 | empty |
| 2 | 389 | 0.65 | 0.79 | 46 | empty |
| 3 | 149 | 0.49 | 0.78 | 28 | empty |
| 4 | 118 | 0.48 | 0.80 | 26 | empty |
| 5 | 194 | 0.46 | 0.74 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–B · 440 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 96 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1WXO · Structure of Archaeal Trans-Editing Protein AlaX in complex with zinc · the same entry in another collection · chain A against A, TM-score 1.00
- O58307 · AlphaFold monomer V2.0 prediction for alanyl-tRNA editing protein alax-S (O58307) · 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 O58307
- Elsewhere: RCSB PDB 1WXO · PDBe 1WXO · UniProt O58307
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