3LX3 | pdb_00003lx3

Plasmodium vivax 6-pyruvoyltetrahydropterin synthase (PTPS) in complex with xanthopterin

• PDB DOI: https://doi.org/10.2210/pdb3LX3/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Plasmodium vivax
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-02-24 Released: 2010-03-09 
• Deposition Author(s): Larson, E.T., Merritt, E.A., Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.167 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Structural analysis of the dual-functional 6-pyruvoyltetrahydropterin synthase from Malaria parasites.

Larson, E.T., Bosch, J., Kim, J.E., Mueller, N., Verlinde, C.L.M.J., Van Voorhis, W.C., Buckner, F.S., Fan, E., Hol, W.G.J., Merritt, E.A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.24 kDa 
• Atom Count: 1,587 
• Modeled Residue Count: 163 
• Deposited Residue Count: 180 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-pyruvoyl tetrahydrobiopterin synthase	A	180	Plasmodium vivax	Mutation(s): 0  Gene Names: PVX_114505 EC: 4.2.3.12
UniProt
Find proteins for A5K2B2 (Plasmodium vivax (strain Salvador I)) Explore A5K2B2  Go to UniProtKB:  A5K2B2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XTN	C [auth A]	2-amino-1,5-dihydropteridine-4,6-dione C6 H5 N5 O2 VURKRJGMSKJIQX-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.167 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.358	α = 90
b = 131.358	β = 90
c = 73.577	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Larson, E.T., Merritt, E.A., Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description