Research workbench
Evolutionary gain of alanine mischarging to non-cognate trnas with a G4:U69 base pair
Analyse Evolutionary gain of alanine mischarging to non-cognate trnas with a G4:U69… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KNN
- Type
- protein
- Length
- 3,585 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine--tRNA ligase, cytoplasmic
- EC
- 6.1.1.7
- UniProt
- P49588
- Ligands
- A5A
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Alanine--tRNA ligase, cytoplasmic (EC 6.1.1.7) | protein | 450 | 46% helix, 18% strand | P49588 |
| C | Alanine--tRNA ligase, cytoplasmic (EC 6.1.1.7) | protein | 444 | 45% helix, 18% strand | P49588 |
| D | Alanine--tRNA ligase, cytoplasmic (EC 6.1.1.7) | protein | 447 | 46% helix, 18% strand | P49588 |
| F, G | Alanine--tRNA ligase, cytoplasmic (EC 6.1.1.7) | protein | 449 | 46% helix, 18% strand | P49588 |
| H | Alanine--tRNA ligase, cytoplasmic (EC 6.1.1.7) | protein | 446 | 46% helix, 17% strand | P49588 |
Ligands and binding sites
- A5A · 5'-O-(N-(L-alanyl)-sulfamoyl)adenosine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.78 | 0.80 | 86 | empty |
| 2 | 894 | 0.76 | 0.79 | 83 | empty |
| 3 | 1083 | 0.74 | 0.77 | 87 | empty |
| 4 | 1010 | 0.74 | 0.77 | 84 | empty |
| 5 | 333 | 0.73 | 0.85 | 39 | A5A |
Interfaces
9 interfaces between chains.
- A–B · 629 Ų buried · 9 hydrogen bonds · protein-protein
- F–H · 545 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 519 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 518 Ų buried · 1 hydrogen bond · protein-protein
- E–G · 506 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5KNN · Evolutionary gain of alanine mischarging to non-cognate tRNAs with a G4:U69 base pair · the same entry in another collection · chain H against H, TM-score 1.00
- P49588 · AlphaFold monomer V2.0 prediction for alanine--tRNA ligase, cytoplasmic (P49588) · a predicted model of the same protein · chain F against A, TM-score 0.98
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 P49588
- Elsewhere: RCSB PDB 5KNN · PDBe 5KNN · UniProt P49588
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