RCSB PDB - 6C86: Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-Lysylsulfamoyl Adenosine

 6C86

Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-Lysylsulfamoyl Adenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.204 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.155 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.156 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-Lysylsulfamoyl Adenosine

Dranow, D.M.Lorimer, D.D.Horanyi, P.S.Edwards, T.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine--tRNA ligase
A, B
535Cryptosporidium parvum Iowa IIMutation(s): 0 
Gene Names: cgd4_2370
EC: 6.1.1.6
UniProt
Find proteins for Q5CR27 (Cryptosporidium parvum (strain Iowa II))
Explore Q5CR27 
Go to UniProtKB:  Q5CR27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5CR27
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KAA (Subject of Investigation/LOI)
Query on KAA

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE
C16 H26 N8 O7 S
NARKTLKJPPMFJF-LEJQEAHTSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B],
I [auth B],
J [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
M [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.204 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.155 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.156 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.03α = 90
b = 142.87β = 90
c = 73.24γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted KAAClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description