4YCW

Crystal structure of cladosporin in complex with plasmodium like human lysyl-tRNA synthetase mutant

• PDB DOI: https://doi.org/10.2210/pdb4YCW/pdb

• Classification: ligase/ligase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-02-20 Released: 2015-06-10 
• Deposition Author(s): Fang, P., Wang, J., Guo, M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.268 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 

Literature

Structural Basis for Specific Inhibition of tRNA Synthetase by ATP Competitive Inhibitor

Fang, P., Han, H., Wang, J., Chen, K., Chen, X., Guo, M.

(2015) Chem Biol 22: 1

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 258.21 kDa 
• Atom Count: 16,000 
• Modelled Residue Count: 2,035 
• Deposited Residue Count: 2,220 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine--tRNA ligase	A, B, E, F	513	Homo sapiens	Mutation(s): 0  Gene Names: KARS, KIAA0070 EC: 6.1.1.6
UniProt & NIH Common Fund Data Resources
Find proteins for Q15046 (Homo sapiens) Explore Q15046  Go to UniProtKB:  Q15046
PHAROS:  Q15046 GTEx:  ENSG00000065427

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminoacyl tRNA synthase complex-interacting multifunctional protein 2	C, D, G, H	42	Homo sapiens	Mutation(s): 0  Gene Names: AIMP2, JTV1, PRO0992
UniProt & NIH Common Fund Data Resources
Find proteins for Q13155 (Homo sapiens) Explore Q13155  Go to UniProtKB:  Q13155
PHAROS:  Q13155 GTEx:  ENSG00000106305

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KRS	J [auth A], L [auth B], N [auth E], P [auth F]	cladosporin C16 H20 O5 WOMKDMUZNBFXKG-ZWKOPEQDSA-N
LYS	I [auth A], K [auth B], M [auth E], O [auth F]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O

Binding Affinity Annotations
ID	Source	Binding Affinity
KRS	BindingDB:  4YCW	IC50: min: 2.00e+4, max: 1.05e+5 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.268 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.283	α = 90.8
b = 75.561	β = 99.09
c = 162.987	γ = 109.83

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-06-10 
Deposition Author(s): Fang, P., Wang, J., Guo, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM100136
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM106134

Revision History  

• Version 1.0: 2015-06-10
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description