9YV3 | pdb_00009yv3

Crystal Structure of a ternary complex of Saccharomyces cerevisiae Sec14 with a small molecule inhibitor and phosphatidylcholine

• PDB DOI: https://doi.org/10.2210/pdb9YV3/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-10-23 Released: 2025-11-05 
• Deposition Author(s): Singh, P.K., Green, S.M., Krieger, I., Sacchettini, J., Igumenova, T.I., Bankaitis, V.A.
• Funding Organization(s): Welch Foundation, Robert A. Welch Foundation, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.268 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a ternary complex of Saccharomyces cerevisiae Sec14 with a small molecule inhibitor and phosphatidylcholine

Singh, P.K., Green, S.M., Krieger, I., Sacchettini, J., Igumenova, T.I., Bankaitis, V.A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.42 kDa 
• Atom Count: 2,700 
• Modeled Residue Count: 298 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SEC14 cytosolic factor	A	298	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SEC14, PIT1, YMR079W, YM9582.04
UniProt
Find proteins for P24280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P24280  Go to UniProtKB:  P24280

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
POV (Subject of Investigation/LOI)	B [auth A]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C42 H82 N O8 P WTJKGGKOPKCXLL-PFDVCBLKSA-N
IUO (Subject of Investigation/LOI)	C [auth A]	(4-chloranyl-3-nitro-phenyl)-[4-(2-fluorophenyl)piperazin-1-yl]methanone C17 H15 Cl F N3 O3 LSPJXCGEFJDMHA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.268 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.24	α = 90
b = 89.24	β = 90
c = 100.38	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Singh, P.K., Green, S.M., Krieger, I., Sacchettini, J., Igumenova, T.I., Bankaitis, V.A.

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Funding Organization	Location	Grant Number
Welch Foundation	United States	A-2194-20240404
Robert A. Welch Foundation	United States	BE-0017
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	NIH R35 GM131804
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	NIH RO1 GM108998

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release