9ZK4 | pdb_00009zk4

Crystal structure of a malonate bound C2 domain containing protein from Trichomonas vaginalis (P21 form)

• PDB DOI: https://doi.org/10.2210/pdb9ZK4/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Trichomonas vaginalis G3
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-12-05 Released: 2025-12-17 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.171 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.143 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of a malonate bound C2 domain containing protein from Trichomonas vaginalis (P21 form)

Liu, L., Lovell, S., Battaile, K.P., Buchko, G.W.

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.06 kDa 
• Atom Count: 2,521 
• Modeled Residue Count: 272 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C2 domain containing protein	A, B	143	Trichomonas vaginalis G3	Mutation(s): 0  Gene Names: TVAG_002900
UniProt
Find proteins for A2EZR3 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore A2EZR3  Go to UniProtKB:  A2EZR3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	C [auth A], F [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.171 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.143 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M39ZK4

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.206	α = 90
b = 82.36	β = 96.61
c = 56.78	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release