9H5R | pdb_00009h5r

X-ray structure of Trichomonas vaginalis inactive mutant hydrogenosomal processing peptidase heterodimer (HPPin)

• PDB DOI: https://doi.org/10.2210/pdb9H5R/pdb

• Classification: HYDROLASE
• Organism(s): Trichomonas vaginalis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-10-23 Released: 2025-11-05 
• Deposition Author(s): Samad, A., Cianci, M., Motlova, L., Barinka, C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 
  0.273 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of Trichomonas vaginalis inactive mutant hydrogenosomal processing peptidase heterodimer (HPPin)

Samad, A., Cianci, M., Motlova, L., Barinka, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 95 kDa 
• Atom Count: 6,462 
• Modeled Residue Count: 812 
• Deposited Residue Count: 850 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-MPP	A	431	Trichomonas vaginalis	Mutation(s): 0  Gene Names: TVAG_119710
UniProt
Find proteins for A2D7B7 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore A2D7B7  Go to UniProtKB:  A2D7B7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Clan ME, family M16, insulinase-like metallopeptidase	B	419	Trichomonas vaginalis	Mutation(s): 1  Gene Names: TVAG_233350
UniProt
Find proteins for A2ES04 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore A2ES04  Go to UniProtKB:  A2ES04

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free:  0.273 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.91	α = 90
b = 115.1	β = 90
c = 125.115	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Samad, A., Cianci, M., Motlova, L., Barinka, C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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