9MED | pdb_00009med

Crystal Structure Pyrophosphate-fructose 6-phosphate 1-phosphotransferase 1 (Pfk1) from Trichomonas vaginalis (AMP/beta-D-Glucose-6-phosphate complex)

PDB DOI: https://doi.org/10.2210/pdb9MED/pdb

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

Deposited: 2024-12-06 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: 2.62 Å
R-Value Free:
0.234 (Depositor), 0.234 (DCC)
R-Value Work:
0.192 (Depositor), 0.197 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure Pyrophosphate-fructose 6-phosphate 1-phosphotransferase 1 (Pfk1) from Trichomonas vaginalis (AMP/beta-D-Glucose-6-phosphate complex)

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

To be published.

Macromolecule Content

Total Structure Weight: 193.5 kDa
Atom Count: 13,064
Modeled Residue Count: 1,680
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 6 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 P [auth C] SDF format, chain U [auth D] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain P [auth C] mmCIF format, chain U [auth D] mmCIF format, chain J [auth B]	F [auth A], J [auth B], P [auth C], U [auth D]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain U [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain U [auth D]
BG6 (Subject of Investigation/LOI) Query on BG6 Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain Q [auth C] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth C]	K [auth B], Q [auth C]	6-O-phosphono-beta-D-glucopyranose C₆ H₁₃ O₉ P NBSCHQHZLSJFNQ-VFUOTHLCSA-N		Interactions Focus chain K [auth B] Focus chain Q [auth C] Interactions & Density Focus chain K [auth B] Focus chain Q [auth C]
PPV (Subject of Investigation/LOI) Query on PPV 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]	PYROPHOSPHATE H₄ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain T [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain T [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D] mmCIF format, chain T [auth C]	E [auth A] H [auth A] L [auth B] M [auth B] N [auth B] E [auth A], H [auth A], L [auth B], M [auth B], N [auth B], R [auth C], S [auth C], T [auth C], V [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain O [auth C] MOL2 format, chain O [auth C] mmCIF format, chain O [auth C]	O [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain O [auth C] Interactions & Density Focus chain O [auth C]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free: 0.234 (Depositor), 0.234 (DCC)
R-Value Work: 0.192 (Depositor), 0.197 (DCC)
R-Value Observed: 0.194 (Depositor)

Diffraction Data: https://doi.org/10.18430/M39MED

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.875	α = 90
b = 86.875	β = 90
c = 475.979	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