3ENZ

Arsenolytic structure of Plasmodium falciparum purine nucleoside phosphorylase with hypoxanthine, ribose and arsenate ion

PDB DOI: https://doi.org/10.2210/pdb3ENZ/pdb

Classification: TRANSFERASE
Organism(s): Plasmodium falciparum 3D7
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-09-26 Released: 2009-08-04
Deposition Author(s): Chaikuad, A., Brady, R.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.193
R-Value Work: 0.160
R-Value Observed: 0.160

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Conservation of structure and activity in Plasmodium purine nucleoside phosphorylases.

Chaikuad, A., Brady, R.L.

(2009) BMC Struct Biol 9: 42-42

PubMed: 19575810 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/1472-6807-9-42
Primary Citation of Related Structures:
3EMV, 3ENZ

PubMed Abstract:
Purine nucleoside phosphorylase (PNP) is central to purine salvage mechanisms in Plasmodium parasites, the causative agents of malaria. Most human malaria results from infection either by Plasmodium falciparum (Pf), the deadliest form of the parasite, or by the widespread Plasmodium vivax (Pv). Whereas the PNP enzyme from Pf has previously been studied in detail, despite the prevalence of Pv little is known about many of the key metabolic enzymes from this parasite, including PvPNP.

Organizational Affiliation

Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK. Apirat.Chaikuad@sgc.ox.ac.uk

Macromolecule Content

Total Structure Weight: 171.45 kDa
Atom Count: 12,047
Modelled Residue Count: 1,465
Deposited Residue Count: 1,518
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase	A, B, C, D, E A, B, C, D, E, F	253	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: PFE0660c EC: 2.4.2.1
UniProt
Find proteins for Q8I3X4 (Plasmodium falciparum (isolate 3D7)) Explore Q8I3X4 Go to UniProtKB: Q8I3X4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8I3X4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ART Query on ART Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain JA [auth D] SDF format, chain T [auth B] SDF format, chain TA [auth E] SDF format, chain XA [auth F] SDF format, chain Z [auth C] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain XA [auth F] MOL2 format, chain Z [auth C]	I [auth A] JA [auth D] T [auth B] TA [auth E] XA [auth F] I [auth A], JA [auth D], T [auth B], TA [auth E], XA [auth F], Z [auth C]	ARSENATE As O₄ DJHGAFSJWGLOIV-UHFFFAOYSA-K		Interactions Focus chain I [auth A] Focus chain JA [auth D] Focus chain T [auth B] Focus chain TA [auth E] Focus chain XA [auth F] Focus chain Z [auth C] Interactions & Density Focus chain I [auth A] Focus chain JA [auth D] Focus chain T [auth B] Focus chain TA [auth E] Focus chain XA [auth F] Focus chain Z [auth C]
HPA Query on HPA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain HA [auth D] SDF format, chain R [auth B] SDF format, chain RA [auth E] SDF format, chain VA [auth F] SDF format, chain X [auth C] MOL2 format, chain G [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain VA [auth F] MOL2 format, chain X [auth C]	G [auth A] HA [auth D] R [auth B] RA [auth E] VA [auth F] G [auth A], HA [auth D], R [auth B], RA [auth E], VA [auth F], X [auth C]	HYPOXANTHINE C₅ H₄ N₄ O FDGQSTZJBFJUBT-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain HA [auth D] Focus chain R [auth B] Focus chain RA [auth E] Focus chain VA [auth F] Focus chain X [auth C] Interactions & Density Focus chain G [auth A] Focus chain HA [auth D] Focus chain R [auth B] Focus chain RA [auth E] Focus chain VA [auth F] Focus chain X [auth C]
R1X Query on R1X Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain IA [auth D] SDF format, chain S [auth B] SDF format, chain SA [auth E] SDF format, chain WA [auth F] SDF format, chain Y [auth C] MOL2 format, chain H [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain WA [auth F] MOL2 format, chain Y [auth C]	H [auth A] IA [auth D] S [auth B] SA [auth E] WA [auth F] H [auth A], IA [auth D], S [auth B], SA [auth E], WA [auth F], Y [auth C]	1,4-anhydro-D-ribitol C₅ H₁₀ O₄ KZVAAIRBJJYZOW-LMVFSUKVSA-N		Interactions Focus chain H [auth A] Focus chain IA [auth D] Focus chain S [auth B] Focus chain SA [auth E] Focus chain WA [auth F] Focus chain Y [auth C] Interactions & Density Focus chain H [auth A] Focus chain IA [auth D] Focus chain S [auth B] Focus chain SA [auth E] Focus chain WA [auth F] Focus chain Y [auth C]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth F] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain U [auth B] SDF format, chain UA [auth E] SDF format, chain V [auth B] SDF format, chain YA [auth F] SDF format, chain ZA [auth F] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain YA [auth F] MOL2 format, chain ZA [auth F]	AA [auth C] AB [auth F] BA [auth C] CA [auth C] DA [auth C] AA [auth C], AB [auth F], BA [auth C], CA [auth C], DA [auth C], EA [auth C], FA [auth C], J [auth A], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], NA [auth D], O [auth A], OA [auth D], P [auth A], U [auth B], UA [auth E], V [auth B], YA [auth F], ZA [auth F]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain YA [auth F] Focus chain ZA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain YA [auth F] Focus chain ZA [auth F]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain PA [auth D] SDF format, chain Q [auth A] SDF format, chain QA [auth D] SDF format, chain W [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain W [auth B]	GA [auth C], PA [auth D], Q [auth A], QA [auth D], W [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain GA [auth C] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain W [auth B] Interactions & Density Focus chain GA [auth C] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain W [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.193
R-Value Work: 0.160
R-Value Observed: 0.160
Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.82	α = 90
b = 177.82	β = 90
c = 253.868	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-08-04

Deposition Author(s):

Chaikuad, A.

Brady, R.L.

Revision History (Full details and data files)

Version 1.0: 2009-08-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations
Version 2.1: 2023-09-06
Changes: Data collection, Database references, Refinement description