MolNFT v1 · #26398 · protein
Structure of archaeal trans-editing protein alax in complex with L- serine
1WNU · Alanyl-tRNA synthetase: “Structure of archaeal trans-editing protein alax in complex with L- serine”. X-ray diffraction, 2 ligands (SER, ZN), 6 pockets (best druggability 0.55). MolNFT v1 #26398 on GenesisL1: 3D structure, binding…
- PDB
- 1WNU
- Type
- protein
- Length
- 306 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanyl-tRNA synthetase
- UniProt
- O58307
- Ligands
- SER, ZN
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanyl-tRNA synthetase | protein | 154 | 35% helix, 32% strand | O58307 |
| B | Alanyl-tRNA synthetase | protein | 152 | 36% helix, 33% strand | O58307 |
Ligands and binding sites
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 | 234 | 0.55 | 0.78 | 32 | SER |
| 2 | 175 | 0.53 | 0.79 | 27 | SER |
| 3 | 108 | 0.41 | 0.77 | 18 | empty |
| 4 | 62 | 0.34 | 0.77 | 16 | empty |
| 5 | 65 | 0.34 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 601 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 1WNU · Structure of Archaeal Trans-Editing Protein AlaX in complex with L-serine · 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 B 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 1WNU · PDBe 1WNU · UniProt O58307
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