9ZK6 | pdb_00009zk6

Crystal structure of a C2 domain containing protein from Trichomonas vaginalis in complex with pyrophosphate

PDB DOI: https://doi.org/10.2210/pdb9ZK6/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.231 (Depositor), 0.233 (DCC)
R-Value Work:
0.211 (Depositor), 0.214 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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Literature

Crystal structure of a C2 domain containing protein from Trichomonas vaginalis in complex with pyrophosphate

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

To be published.

Macromolecule Content

Total Structure Weight: 33.12 kDa
Atom Count: 2,126
Modeled Residue Count: 251
Deposited Residue Count: 286
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A2EZR3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PPV (Subject of Investigation/LOI) Query on PPV Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	PYROPHOSPHATE H₄ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.231 (Depositor), 0.233 (DCC)
R-Value Work: 0.211 (Depositor), 0.214 (DCC)
R-Value Observed: 0.212 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.518	α = 90
b = 89.297	β = 90
c = 96.105	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-17

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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 (Full details and data files)

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

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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.