1Y13 | pdb_00001y13

Structural Analysis of Plasmodium falciparum 6-pyruvoyl tetrahydropterin synthase (PTPS)

• PDB DOI: https://doi.org/10.2210/pdb1Y13/pdb

• Classification: LYASE, BIOSYNTHETIC PROTEIN
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-11-17 Released: 2005-01-04 
• Deposition Author(s): Bosch, J., Hol, W.G.J., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.235 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

Structural Analysis of Plasmodium falciparum 6-pyruvoyl tetrahydropterin synthase (PTPS)

Bosch, J., Hol, W.G.J., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 64.41 kDa 
• Atom Count: 4,150 
• Modeled Residue Count: 489 
• Deposited Residue Count: 543 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-pyruvoyl tetrahydropterin synthase	A, B, C	181	Plasmodium falciparum	Mutation(s): 1  EC: 4.2.3.12
UniProt
Find proteins for C6KTB6 (Plasmodium falciparum (isolate 3D7)) Explore C6KTB6  Go to UniProtKB:  C6KTB6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BIO	E [auth A], G [auth B], I [auth C]	BIOPTERIN C9 H11 N5 O3 LHQIJBMDNUYRAM-AWFVSMACSA-N
ZN	D [auth A], F [auth B], H [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.235 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.319	α = 90
b = 103.319	β = 90
c = 131.111	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-04 
Deposition Author(s): Bosch, J., Hol, W.G.J., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History  

• Version 1.0: 2005-01-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Refinement description, Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary