5ZYL | pdb_00005zyl

Crystal structure of CERT START domain in complex with compound E25A

PDB DOI: https://doi.org/10.2210/pdb5ZYL/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:
0.224 (Depositor), 0.224 (DCC)
R-Value Work:
0.174 (Depositor), 0.174 (DCC)
R-Value Observed:
0.177 (Depositor)

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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: 27.6 kDa
Atom Count: 2,297
Modeled Residue Count: 235
Deposited Residue Count: 237
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y5P4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9MC (Subject of Investigation/LOI) Query on 9MC 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-[4-cyclopentyl-3-[(1~{S},2~{R})-2-pyridin-2-ylcyclopropyl]phenyl]phenyl]sulfonylethanol C₂₇ H₂₉ N O₃ S SQNBJZZENOHHKX-CLJLJLNGSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.224 (Depositor), 0.224 (DCC)
R-Value Work: 0.174 (Depositor), 0.174 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.006	α = 90
b = 60.006	β = 90
c = 153.455	γ = 90

Software Package:

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

Structure Validation

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.