MolNFT v1 · #117845 · protein
Human mitochondrial tryptophanyl-tRNA synthetase bound by indolmycin and MN*ATP.
5EKD · Tryptophan--tRNA ligase, mitochondrial: “Human mitochondrial tryptophanyl-tRNA synthetase bound by indolmycin and MN*ATP.”. X-ray diffraction, 3 ligands (5BX, ATP, MN), 7 pockets (best druggability 0.77). MolNFT v1 #117845 on…
- PDB
- 5EKD
- Type
- protein
- Length
- 654 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan--tRNA ligase, mitochondrial
- EC
- 6.1.1.2
- UniProt
- Q9UGM6
- Ligands
- 5BX, ATP, MN
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan--tRNA ligase, mitochondrial (EC 6.1.1.2) | protein | 327 | 59% helix, 8% strand | Q9UGM6 |
| B | Tryptophan--tRNA ligase, mitochondrial (EC 6.1.1.2) | protein | 327 | 58% helix, 8% strand | Q9UGM6 |
Ligands and binding sites
- 5BX · (5S)-5-[(1R)-1-(1H-indol-3-yl)ethyl]-2-(methylamino)-1,3-oxazol-4(5H)-one · ligand · 2 copies · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.77 | 0.84 | 54 | 5BX, ATP, MN |
| 2 | 455 | 0.76 | 0.85 | 45 | 5BX, ATP, MN |
| 3 | 75 | 0.76 | 0.99 | 16 | GOL |
| 4 | 82 | 0.41 | 0.79 | 16 | empty |
| 5 | 80 | 0.39 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1986 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5EKD · Human mitochondrial tryptophanyl-tRNA synthetase bound by indolmycin and Mn*ATP. · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UGM6 · AlphaFold monomer V2.0 prediction for tryptophan--tRNA ligase, mitochondrial (Q9UGM6) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9UGM6
- Elsewhere: RCSB PDB 5EKD · PDBe 5EKD · UniProt Q9UGM6
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