Research workbench
Fragment of human mitochondrial alanyl-tRNA synthetase C-ala domain
Analyse Fragment of human mitochondrial alanyl-tRNA synthetase C-ala domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NLY
- Type
- protein
- Length
- 717 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine--tRNA ligase, mitochondrial
- EC
- 6.1.1.7
- UniProt
- Q5JTZ9
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Alanine--tRNA ligase, mitochondrial (EC 6.1.1.7) | protein | 178 | 56% helix, 17% strand | Q5JTZ9 |
| A | Alanine--tRNA ligase, mitochondrial (EC 6.1.1.7) | protein | 181 | 59% helix, 17% strand | Q5JTZ9 |
| C | Alanine--tRNA ligase, mitochondrial (EC 6.1.1.7) | protein | 176 | 60% helix, 17% strand | Q5JTZ9 |
| D | Alanine--tRNA ligase, mitochondrial (EC 6.1.1.7) | protein | 182 | 59% helix, 16% strand | Q5JTZ9 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.70 | 0.84 | 47 | empty |
| 2 | 444 | 0.63 | 0.77 | 45 | empty |
| 3 | 134 | 0.48 | 0.78 | 26 | empty |
| 4 | 77 | 0.41 | 0.79 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–D · 796 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 784 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 534 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 342 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 239 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6NLY · Fragment of human mitochondrial Alanyl-tRNA Synthetase C-Ala domain · the same entry in another collection · chain D against D, TM-score 1.00
- Q5JTZ9 · AlphaFold monomer V2.0 prediction for alanine--tRNA ligase, mitochondrial (Q5JTZ9) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q5JTZ9
- Elsewhere: RCSB PDB 6NLY · PDBe 6NLY · UniProt Q5JTZ9
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