3EZ3 | pdb_00003ez3

Crystal Structure of Plasmodium vivax geranylgeranylpyrophosphate synthase PVX_092040 with zoledronate and IPP bound

PDB DOI: https://doi.org/10.2210/pdb3EZ3/pdb

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

Deposited: 2008-10-22 Released: 2008-12-02
Deposition Author(s): Wernimont, A.K., 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:
0.291 (Depositor), 0.280 (DCC)
R-Value Work:
0.226 (Depositor), 0.220 (DCC)
R-Value Observed:
0.229 (Depositor)

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 geranylgeranylpyrophosphate synthase PVX_092040 with zoledronate and IPP bound

Wernimont, A.K., 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: 187.63 kDa
Atom Count: 12,384
Modeled Residue Count: 1,419
Deposited Residue Count: 1,584
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyl pyrophosphate synthase, putative	A, B, C, D	396	Plasmodium vivax	Mutation(s): 0 Gene Names: 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZOL Query on ZOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain S [auth C] SDF format, chain X [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain S [auth C] mmCIF format, chain X [auth D]	E [auth A], L [auth B], S [auth C], X [auth D]	ZOLEDRONIC ACID C₅ H₁₀ N₂ O₇ P₂ XRASPMIURGNCCH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain X [auth D]
IPE Query on IPE Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain T [auth C] SDF format, chain Y [auth D] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D]	F [auth A], M [auth B], T [auth C], Y [auth D]	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE C₅ H₁₂ O₇ P₂ NUHSROFQTUXZQQ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain F [auth A] Focus chain M [auth B] Focus chain T [auth C] Focus chain Y [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain K [auth A] SDF format, chain Q [auth B] MOL2 format, chain CA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain CA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B]	CA [auth D], K [auth A], Q [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain K [auth A] Focus chain Q [auth B] Interactions & Density Focus chain CA [auth D] Focus chain K [auth A] Focus chain Q [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain R [auth B] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] mmCIF format, chain J [auth A] mmCIF format, chain R [auth B]	J [auth A], R [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain R [auth B] Interactions & Density Focus chain J [auth A] Focus chain R [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain Z [auth D]	AA [auth D] BA [auth D] G [auth A] H [auth A] I [auth A] AA [auth D], BA [auth D], G [auth A], H [auth A], I [auth A], N [auth B], O [auth B], P [auth B], U [auth C], V [auth C], W [auth C], Z [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.291 (Depositor), 0.280 (DCC)
R-Value Work: 0.226 (Depositor), 0.220 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.266	α = 90
b = 109.696	β = 90
c = 139.529	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-12-02

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2008-12-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Advisory, Refinement description
Version 1.3: 2023-12-27
Changes: Advisory, Data collection, Database references, Derived calculations