6KO9

Crystal structure of the Gefitinib Intermediate 1 bound RamR determined with XtaLAB Synergy


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Development of a structure determination method using a multidrug-resistance regulator protein as a framework.

Matsumoto, T.Nakashima, R.Yamano, A.Nishino, K.

(2019) Biochem.Biophys.Res.Commun. 518: 402-408

  • DOI: 10.1016/j.bbrc.2019.08.070
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure determination of organic compounds is desirable for the development of medicines, aroma chemicals, and agricultural chemicals. However, the crystallization of organic compounds is often troublesome, because crystallization requires a re ...

    The structure determination of organic compounds is desirable for the development of medicines, aroma chemicals, and agricultural chemicals. However, the crystallization of organic compounds is often troublesome, because crystallization requires a relatively large quantity of high purity compounds and crystallization trials often need to be performed repetitively using different conditions. Some proteins are known to be able to bind to various organic compounds. The multidrug-resistance regulator protein RamR is one such protein. We have developed a structure determination method for organic compounds using RamR. RamR bound to organic compounds, including one compound that was not a known ligand for RamR, and the structures of the complexes were successfully determined. Because the RamR crystal is hydrophilic, this method may be useful for compounds that cannot be handled by the crystalline sponge method.


    Organizational Affiliation

    Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima, Tokyo, 196-8666, Japan.,Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan.,Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima, Tokyo, 196-8666, Japan. Electronic address: t-matumo@rigaku.co.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative regulatory protein
A, B, C, D
194Salmonella typhimurium (strain 14028s / SGSC 2262)Mutation(s): 0 
Find proteins for A0A0F6AY66 (Salmonella typhimurium (strain 14028s / SGSC 2262))
Go to UniProtKB:  A0A0F6AY66
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XZ1
Query on XZ1

Download SDF File 
Download CCD File 
A, B, C, D
4-[(3-chloranyl-4-fluoranyl-phenyl)amino]-7-methoxy-quinazolin-6-ol
C15 H11 Cl F N3 O2
JLVTVCRXFMLUIF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.220 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 43.513α = 74.64
b = 54.792β = 81.94
c = 92.224γ = 89.98
Software Package:
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
REFMACrefinement
CrysalisProdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-10-09
    Type: Initial release