5ZYH | pdb_00005zyh

Crystal structure of CERT START domain in complex with compound E5

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.252 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.214 (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 9N0Click on this verticalbar to view details

This is version 1.2 of the entry. See complete history. 


Literature

Natural ligand-nonmimetic inhibitors of the lipid-transfer protein CERT

Nakao, N., Ueno, M., Sakai, S., Egawa, D., Hanzawa, H., Kawasaki, S., Kumagai, K., Suzuki, M., Kobayashi, S., Hanada, K.

(2019) Commun Chem 


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LIPID-TRANSFER PROTEIN CERT237Homo sapiensMutation(s): 0 
Gene Names: CERT
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5P4 (Homo sapiens)
Explore Q9Y5P4 
Go to UniProtKB:  Q9Y5P4
PHAROS:  Q9Y5P4
GTEx:  ENSG00000113163 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y5P4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9N0 (Subject of Investigation/LOI)
Query on 9N0
Download Ideal Coordinates CCD File 
B [auth A]2-[4-[3-~{tert}-butyl-5-[(1~{R},2~{S})-2-pyridin-2-ylcyclopropyl]phenyl]phenyl]sulfonylethanol
C26 H29 N O3 S
KGSAEQLILKLRSG-ZEQRLZLVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.09α = 90
b = 60.09β = 90
c = 153.77γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
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 9N0Click on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references