3CC9

Crystal structure of Plasmodium vivax putative polyprenyl pyrophosphate synthase in complex with geranylgeranyl diphosphate

PDB DOI: https://doi.org/10.2210/pdb3CC9/pdb

Classification: LYASE
Organism(s): Plasmodium vivax Sal-1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-02-25 Released: 2008-03-25
Deposition Author(s): Wernimont, A.K., Dunford, J., Lew, J., Zhao, Y., Kozieradzki, I., Cossar, D., Schapira, M., Bochkarev, A., Arrowsmith, C.H., Bountra, C., Weigelt, J., Edwards, A.M., Hui, R., Artz, J.D., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.296
R-Value Work: 0.241
R-Value Observed: 0.243

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Plasmodium vivax putative polyprenyl pyrophosphate synthase in complex with geranylgeranyl diphosphate.

Wernimont, A.K., Dunford, J., Lew, J., Zhao, Y., Kozieradzki, I., Cossar, D., Schapira, M., Bochkarev, A., Arrowsmith, C.H., Bountra, C., Weigelt, J., Edwards, A.M., Hui, R., Artz, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 186.69 kDa
Atom Count: 11,221
Modelled Residue Count: 1,371
Deposited Residue Count: 1,584
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative farnesyl pyrophosphate synthase	A, B, C, D	396	Plasmodium vivax Sal-1	Mutation(s): 0 Gene Names: PF11_0295, PVX_092040
UniProt
Find proteins for A5K4U6 (Plasmodium vivax (strain Salvador I)) Explore A5K4U6 Go to UniProtKB: A5K4U6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5K4U6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GRG Query on GRG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain I [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain I [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth C] mmCIF format, chain I [auth D]	F [auth A], G [auth B], H [auth C], I [auth D]	GERANYLGERANYL DIPHOSPHATE C₂₀ H₃₆ O₇ P₂ OINNEUNVOZHBOX-QIRCYJPOSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.296
R-Value Work: 0.241
R-Value Observed: 0.243
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.095	α = 90
b = 108.985	β = 90
c = 141.354	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-03-25

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2008-03-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description

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3CC9

Crystal structure of Plasmodium vivax putative polyprenyl pyrophosphate synthase in complex with geranylgeranyl diphosphate

Crystal structure of Plasmodium vivax putative polyprenyl pyrophosphate synthase in complex with geranylgeranyl diphosphate.

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)