Research workbench
Human mitochondrial alanyl-tRNA synthetase C-terminal domain
Analyse Human mitochondrial alanyl-tRNA synthetase C-terminal domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NLQ
- Type
- protein
- Length
- 421 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
- Ligands
- CA
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Alanine--tRNA ligase, mitochondrial (EC 6.1.1.7) | protein | 105 | 41% helix, 29% strand | Q5JTZ9 |
| B | Alanine--tRNA ligase, mitochondrial (EC 6.1.1.7) | protein | 106 | 41% helix, 28% strand | Q5JTZ9 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1169 | 0.77 | 0.79 | 108 | empty |
| 2 | 88 | 0.32 | 0.73 | 17 | empty |
Interfaces
4 interfaces between chains.
- B–C · 480 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 359 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 280 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 173 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6NLQ · Human Mitochondrial Alanyl-tRNA Synthetase C-terminal domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q5JTZ9 · AlphaFold monomer V2.0 prediction for alanine--tRNA ligase, mitochondrial (Q5JTZ9) · a predicted model of the same protein · chain B 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 Q5JTZ9
- Elsewhere: RCSB PDB 6NLQ · PDBe 6NLQ · UniProt Q5JTZ9
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