9MEC | pdb_00009mec

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

PDB DOI: https://doi.org/10.2210/pdb9MEC/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: 2.80 Å
R-Value Free:
0.237 (Depositor), 0.236 (DCC)
R-Value Work:
0.200 (Depositor), 0.204 (DCC)
R-Value Observed:
0.202 (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 of Pyrophosphate-fructose 6-phosphate 1-phosphotransferase 1 (Pfk1) from Trichomonas vaginalis (AMP/alpha-D-Glucose-6-phosphate complex)

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

To be published.

Macromolecule Content

Total Structure Weight: 193.6 kDa
Atom Count: 13,092
Modeled Residue Count: 1,685
Deposited Residue Count: 1,736
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O61068
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 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 E [auth A] SDF format, chain N [auth B] SDF format, chain V [auth D] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain V [auth D] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain N [auth B] mmCIF format, chain V [auth D] mmCIF format, chain F [auth A]	E [auth A], F [auth A], N [auth B], V [auth D]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain N [auth B] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain N [auth B] Focus chain V [auth D]
G6P (Subject of Investigation/LOI) Query on G6P Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth B] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B]	I [auth A], O [auth B]	6-O-phosphono-alpha-D-glucopyranose C₆ H₁₃ O₉ P NBSCHQHZLSJFNQ-DVKNGEFBSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Interactions & Density Focus chain I [auth A] Focus chain O [auth B]
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 J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain W [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D]	J [auth A] K [auth A] P [auth B] Q [auth B] R [auth B] J [auth A], K [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth C], U [auth C], W [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.237 (Depositor), 0.236 (DCC)
R-Value Work: 0.200 (Depositor), 0.204 (DCC)
R-Value Observed: 0.202 (Depositor)

Diffraction Data:

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.909	α = 90
b = 86.909	β = 90
c = 473.809	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

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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