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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine--tRNA ligase
A, B, E, F
513Homo sapiensMutation(s): 0 
Gene Names: KARSKIAA0070
EC: 6.1.1.6 (PDB Primary Data), 2.7.7 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q15046 (Homo sapiens)
Explore Q15046 
Go to UniProtKB:  Q15046
PHAROS:  Q15046
GTEx:  ENSG00000065427 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15046
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
C, D, G, H
42Homo sapiensMutation(s): 0 
Gene Names: AIMP2JTV1PRO0992
UniProt & NIH Common Fund Data Resources
Find proteins for Q13155 (Homo sapiens)
Explore Q13155 
Go to UniProtKB:  Q13155
PHAROS:  Q13155
GTEx:  ENSG00000106305 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13155
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KRS
Query on KRS

Download Ideal Coordinates CCD File 
J [auth A],
L [auth B],
N [auth E],
P [auth F]
cladosporin
C16 H20 O5
WOMKDMUZNBFXKG-ZWKOPEQDSA-N
LYS
Query on LYS

Download Ideal Coordinates CCD File 
I [auth A],
K [auth B],
M [auth E],
O [auth F]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
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

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Ligand Structure Quality Assessment 


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  (Full details and data files)

  • 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