5ZYG | pdb_00005zyg

Crystal structure of CERT START domain in complex with compound B5

PDB DOI: https://doi.org/10.2210/pdb5ZYG/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.226 (Depositor), 0.230 (DCC)
R-Value Work:
0.192 (Depositor), 0.190 (DCC)
R-Value Observed:
0.194 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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

Macromolecule Content

Total Structure Weight: 27.48 kDa
Atom Count: 2,155
Modelled Residue Count: 233
Deposited Residue Count: 237
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y5P4
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9N3 Query on 9N3 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-[4-[3-~{tert}-butyl-5-(2-pyridin-2-ylethyl)phenyl]phenyl]sulfonylethanol C₂₅ H₂₉ N O₃ S MDYWYEIFJBZYTD-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.226 (Depositor), 0.230 (DCC)
R-Value Work: 0.192 (Depositor), 0.190 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.77	α = 90
b = 59.77	β = 90
c = 154.45	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-02-27

Deposition Author(s):

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.