Research workbench
Crystal structure of archaeoglobus fulgidus alanyl-tRNA synthetase in complex with wild-type TRNA(ALA) having G3.U70
Analyse Crystal structure of archaeoglobus fulgidus alanyl-tRNA synthetase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WQY
- Type
- protein + RNA
- Length
- 1,885 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine--tRNA ligase; RNA (75-mer)
- EC
- 6.1.1.7
- UniProt
- O28029
- Ligands
- A5A, MG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanine--tRNA ligase (EC 6.1.1.7) | protein | 905 | 41% helix, 23% strand | O28029 |
| B | Alanine--tRNA ligase (EC 6.1.1.7) | protein | 905 | 41% helix, 23% strand | O28029 |
| C | RNA (75-mer) | rna | 75 | — | — |
Ligands and binding sites
- A5A · 5'-O-(N-(L-alanyl)-sulfamoyl)adenosine · ligand · 2 copies · chains A, C, B
- MG · Magnesium ion · metal · 3 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.77 | 0.80 | 68 | A5A |
| 2 | 917 | 0.75 | 0.78 | 73 | empty |
| 3 | 792 | 0.73 | 0.78 | 70 | empty |
| 4 | 823 | 0.73 | 0.78 | 65 | empty |
| 5 | 122 | 0.72 | 0.92 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2451 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 2034 Ų buried · 49 hydrogen bonds · protein-nucleic
- B–C · 132 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 3WQY · Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- O28029 · AlphaFold monomer V2.0 prediction for alanine--tRNA ligase (O28029) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 O28029
- Elsewhere: RCSB PDB 3WQY · PDBe 3WQY · UniProt O28029
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.