9H6R | pdb_00009h6r

X-ray structure of Hydrogenosomal processing peptidase (HPP), E56Q inactive mutant, from Trichomonas vaginalis co-crystallized with presequence peptide from ferredoxin oxidoreductase (PFO) - not visible in the structure model

PDB DOI: https://doi.org/10.2210/pdb9H6R/pdb

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

Deposited: 2024-10-25 Released: 2025-11-05
Deposition Author(s): Samad, A., Barinka, C., Motlova, L., Cianci, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.240 (Depositor), 0.243 (DCC)
R-Value Work:
0.186 (Depositor), 0.189 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

X-ray structure of Hydrogenosomal processing peptidase (HPP), E56Q inactive mutant, from Trichomonas vaginalis co-crystallized with presequence peptide from ferredoxin oxidoreductase (PFO) - not visible in the structure model

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

To be published.

Macromolecule Content

Total Structure Weight: 95.19 kDa
Atom Count: 6,510
Modeled Residue Count: 809
Deposited Residue Count: 850
Unique protein chains: 2

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A2D7B7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A2ES04
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] I [auth B] C [auth A], D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]