Download MendeleyBinding of Mg2+ATP Enhances Inhibition of Human Mitochondrial Tryptophanyl-tRNA Synthetase by Indolmycin
Williams, T.L., Carter Jr., C.W.To be published.
5EKD
Human mitochondrial tryptophanyl-tRNA synthetase bound by indolmycin and Mn*ATP.
- PDB DOI: https://doi.org/10.2210/pdb5EKD/pdb
- Classification: LIGASE/ANTIBIOTIC
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2015-11-03 Released: 2016-11-16
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.82 Å
- R-Value Free: 0.207
- R-Value Work: 0.170
- R-Value Observed: 0.172
Starting Model: experimental
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This is version 1.4 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Tryptophan--tRNA ligase, mitochondrial | 343 | Homo sapiens | Mutation(s): 0 Gene Names: WARS2 EC: 6.1.1.2 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9UGM6 (Homo sapiens) Explore Q9UGM6 Go to UniProtKB: Q9UGM6 | |||||
PHAROS: Q9UGM6 GTEx: ENSG00000116874 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9UGM6 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ATP Query on ATP | D [auth A], H [auth B] | ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N |  | ||
| 5BX Query on 5BX | C [auth A], G [auth B] | (5S)-5-[(1R)-1-(1H-indol-3-yl)ethyl]-2-(methylamino)-1,3-oxazol-4(5H)-one C14 H15 N3 O2 GNTVWGDQPXCYBV-PELKAZGASA-N |  | ||
| GOL Query on GOL | K [auth B], L [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| MN Query on MN | E [auth A], F [auth A], I [auth B], J [auth B] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.82 Å
- R-Value Free: 0.207
- R-Value Work: 0.170
- R-Value Observed: 0.172
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 58.289 | α = 90 |
| b = 78.087 | β = 96.55 |
| c = 153.996 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| SCALA | data scaling |
| Coot | model building |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-11-16 Deposition Author(s): Williams, T.L., Carter Jr., C.W.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM40906 |
Revision History (Full details and data files)
- Version 1.0: 2016-11-16
Type: Initial release - Version 1.1: 2016-12-07
Changes: Structure summary - Version 1.2: 2017-09-20
Changes: Author supporting evidence - Version 1.3: 2019-12-25
Changes: Author supporting evidence, Derived calculations - Version 1.4: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
