5ZYK

Crystal structure of CERT START domain in complex with compound E25

• PDB DOI: https://doi.org/10.2210/pdb5ZYK/pdb

• Classification: LIPID TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-05-25 Released: 2019-02-27 
• Deposition Author(s): Suzuki, M., Nakao, N., Ueno, M., Sakai, S., Egawa, D., Hanzawa, H., Kawasaki, S., Kumagai, K., Kobayashi, S., Hanada, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.210 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 

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 

• DOI: https://doi.org/10.1038/s42004-019-0118-3

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.5 kDa 
• Atom Count: 2,342 
• Modelled Residue Count: 231 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIPID-TRANSFER PROTEIN CERT	A	237	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9MC (Subject of Investigation/LOI)	B [auth A]	2-[4-[4-cyclopentyl-3-[(1~{S},2~{R})-2-pyridin-2-ylcyclopropyl]phenyl]phenyl]sulfonylethanol C27 H29 N O3 S SQNBJZZENOHHKX-CLJLJLNGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.210 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.13	α = 90
b = 60.13	β = 90
c = 153.59	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-27 
Deposition Author(s): Suzuki, M., Nakao, N., Ueno, M., Sakai, S., Egawa, D., Hanzawa, H., Kawasaki, S., Kumagai, K., Kobayashi, S., Hanada, K.

Revision History  

• 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