9MF6

Crystal Structure of Pyrophosphate-fructose 6-phosphate 1-phosphotransferase 1 (Pfk1) from Trichomonas vaginalis (ADP/5-O-phosphono-alpha-D-ribofuranose complex)

PDB DOI: https://doi.org/10.2210/pdb9MF6/pdb

Classification: TRANSFERASE
Organism(s): Trichomonas vaginalis G3
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-12-09 Released: 2024-12-18
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, 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: 2.65 Å
R-Value Free: 0.263
R-Value Work: 0.208
R-Value Observed: 0.210

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Pyrophosphate-fructose 6-phosphate 1-phosphotransferase 1 (Pfk1) from Trichomonas vaginalis (ADP/5-O-phosphono-alpha-D-ribofuranose complex)

Seibold, S., Liu, L., Lovell, S., Battaile, K.P.

To be published.

Macromolecule Content

Total Structure Weight: 193.01 kDa
Atom Count: 12,626
Modelled Residue Count: 1,678
Deposited Residue Count: 1,736
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1	A, B, C, D	434	Trichomonas vaginalis G3	Mutation(s): 0 Gene Names: Pfk1, TVAG_430830 EC: 2.7.1.90
UniProt
Find proteins for O61068 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore O61068 Go to UniProtKB: O61068
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O61068
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP (Subject of Investigation/LOI) Query on AMP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	F [auth A], G [auth A], K [auth B], L [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B]
HSX (Subject of Investigation/LOI) Query on HSX Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth D]	E [auth A], J [auth B], M [auth C], N [auth D]	5-O-phosphono-alpha-D-ribofuranose C₅ H₁₁ O₈ P KTVPXOYAKDPRHY-AIHAYLRMSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth D]
PPV Query on PPV Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	PYROPHOSPHATE H₄ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.263
R-Value Work: 0.208
R-Value Observed: 0.210
Space Group: P 4₃ 2₁ 2
Diffraction Data: https://doi.org/10.18430/M39MF6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.96	α = 90
b = 86.96	β = 90
c = 473.874	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-12-18

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease

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: 2024-12-18
Type: Initial release

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9MF6

Crystal Structure of Pyrophosphate-fructose 6-phosphate 1-phosphotransferase 1 (Pfk1) from Trichomonas vaginalis (ADP/5-O-phosphono-alpha-D-ribofuranose complex)

Crystal Structure of Pyrophosphate-fructose 6-phosphate 1-phosphotransferase 1 (Pfk1) from Trichomonas vaginalis (ADP/5-O-phosphono-alpha-D-ribofuranose complex)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)