4YCW

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


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 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine--tRNA ligaseA, B, E, F513Homo sapiensMutation(s): 0 
Gene Names: KARSKIAA0070KARS1
EC: 6.1.1.6 (PDB Primary Data), 2.7.7 (UniProt)
Find proteins for Q15046 (Homo sapiens)
Explore Q15046 
Go to UniProtKB:  Q15046
NIH Common Fund Data Resources
PHAROS  Q15046
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Aminoacyl tRNA synthase complex-interacting multifunctional protein 2C, D, G, H42Homo sapiensMutation(s): 0 
Gene Names: AIMP2JTV1PRO0992
Find proteins for Q13155 (Homo sapiens)
Explore Q13155 
Go to UniProtKB:  Q13155
NIH Common Fund Data Resources
PHAROS  Q13155
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KRS
Query on KRS

Download CCD File 
A, B, E, F
cladosporin
C16 H20 O5
WOMKDMUZNBFXKG-ZWKOPEQDSA-N
 Ligand Interaction
LYS
Query on LYS

Download CCD File 
A, B, E, F
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KRSIC50:  20000   nM  BindingDB
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 = 51.283α = 90.8
b = 75.561β = 99.09
c = 162.987γ = 109.83
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM100136
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM106134

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