5QQJ

PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-009-587-558


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.269 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted N6JClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related C3 botulinum toxin substrate 1178Homo sapiensMutation(s): 0 
Gene Names: RAC1TC25MIG5
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P63000 (Homo sapiens)
Explore P63000 
Go to UniProtKB:  P63000
PHAROS:  P63000
GTEx:  ENSG00000136238 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63000
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Kalirin182Homo sapiensMutation(s): 0 
Gene Names: KALRNDUETDUOHAPIPTRAD
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O60229 (Homo sapiens)
Explore O60229 
Go to UniProtKB:  O60229
PHAROS:  O60229
GTEx:  ENSG00000160145 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60229
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N6J
Query on N6J

Download Ideal Coordinates CCD File 
D [auth A]N-{1-[(imidazo[1,2-a]pyridin-2-yl)methyl]-1H-pyrazol-4-yl}-N'-(5-methyl-1,2-oxazol-3-yl)urea
C16 H15 N7 O2
BKMWCTDITJZRHD-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.269 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.568α = 90
b = 62.568β = 90
c = 342.039γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

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 N6JClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references