5EKD | pdb_00005ekd

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
Deposition Author(s): Williams, T.L., Carter Jr., C.W.
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 (Depositor), 0.195 (DCC)
R-Value Work:
0.170 (Depositor), 0.173 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Binding of Mg2+ATP Enhances Inhibition of Human Mitochondrial Tryptophanyl-tRNA Synthetase by Indolmycin

Williams, T.L., Carter Jr., C.W.

To be published.

Macromolecule Content

Total Structure Weight: 78.02 kDa
Atom Count: 5,805
Modeled Residue Count: 654
Deposited Residue Count: 686
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan--tRNA ligase, mitochondrial	A, B	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UGM6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
5BX Query on 5BX Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B]	K [auth B], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain K [auth B] Focus chain L [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], I [auth B], J [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.207 (Depositor), 0.195 (DCC)
R-Value Work: 0.170 (Depositor), 0.173 (DCC)
R-Value Observed: 0.172 (Depositor)

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 Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

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

5EKD | pdb_00005ekd

Human mitochondrial tryptophanyl-tRNA synthetase bound by indolmycin and Mn*ATP.

Literature

Binding of Mg2+ATP Enhances Inhibition of Human Mitochondrial Tryptophanyl-tRNA Synthetase by Indolmycin

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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