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Crystal structure of a C-terminally truncated aspergillus nidulans mitochondrial tyrosyl-tRNA synthetase
Analyse Crystal structure of a C-terminally truncated aspergillus nidulans… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IHX
- Type
- protein
- Length
- 699 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine--tRNA ligase, mitochondrial
- EC
- 6.1.1.1
- UniProt
- Q5BCM1
- Ligands
- TYR
- Pockets
- 13 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine--tRNA ligase, mitochondrial (EC 6.1.1.1) | protein | 360 | 59% helix, 8% strand | Q5BCM1 |
| B | Tyrosine--tRNA ligase, mitochondrial (EC 6.1.1.1) | protein | 339 | 60% helix, 9% strand | Q5BCM1 |
Ligands and binding sites
- TYR · Tyrosine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.67 | 0.78 | 68 | TYR |
| 2 | 217 | 0.63 | 0.83 | 45 | empty |
| 3 | 338 | 0.59 | 0.77 | 35 | empty |
| 4 | 97 | 0.51 | 0.82 | 20 | empty |
| 5 | 114 | 0.41 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 331 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5IHX · Crystal Structure of a C-terminally truncated Aspergillus nidulans mitochondrial… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q5BCM1
- Elsewhere: RCSB PDB 5IHX · PDBe 5IHX · UniProt Q5BCM1
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