Macromolecule Content

Total Structure Weight: 147.07 kDa
Atom Count: 10,510
Modelled Residue Count: 1,176
Deposited Residue Count: 1,248
Unique protein chains: 1

3E15

6-phosphogluconolactonase from Plasmodium vivax

PDB DOI: https://doi.org/10.2210/pdb3E15/pdb

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

Deposited: 2008-08-01 Released: 2008-08-19
Deposition Author(s): Arakaki, T.L., Merritt, E.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.202
R-Value Work: 0.150
R-Value Observed: 0.152

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

6-phosphogluconolactonase from Plasmodium vivax

Arakaki, T.L., Merritt, E.A.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-6-phosphate 1-dehydrogenase	A, B, C, D	312	Plasmodium vivax	Mutation(s): 0 Gene Names: PVX_117790 EC: 3.1.1.31
UniProt
Find proteins for A5K3M1 (Plasmodium vivax (strain Salvador I)) Explore A5K3M1 Go to UniProtKB: A5K3M1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5K3M1
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AZI Query on AZI Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D]	G [auth A], I [auth B], K [auth C], N [auth D]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Ligand Interaction
K Query on K Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D]	F [auth A], H [auth B], J [auth C], M [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth D]	E [auth A], L [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.202
R-Value Work: 0.150
R-Value Observed: 0.152
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.524	α = 63.98
b = 80.846	β = 88.1
c = 89.765	γ = 80.01

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-08-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-08-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-11-13
Changes: Derived calculations, Structure summary

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.