1Y13 Lyase, Biosynthetic Protein date Nov 17, 2004
title Structural Analysis Of Plasmodium Falciparum 6-Pyruvoyl Tetrahydropterin Synthase (Ptps)
authors J.Bosch, W.G.J.Hol, Structural Genomics Of Pathogenic Protozoa Consortium (Sgpp)
compound source
Molecule: 6-Pyruvoyl Tetrahydropterin Synthase
Chain: A, B, C
Synonym: Ptps
Ec: 4.2.3.12
Engineered: Yes
 Organism_scientific: Plasmodium Falciparum
Organism_common: Malaria Parasite P. Falciparum
Organism_taxid: 5833
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21star(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet14b
symmetry Space Group: P 43 21 2
R_factor 0.195 R_Free 0.235
crystal
cell
length a length b length c angle alpha angle beta angle gamma
103.319 103.319 131.111 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand BIO, MSE, ZN enzyme Lyase E.C.4.2.3.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (91 Kb) [Save to disk]
  • Biological Unit Coordinates (1y13.pdb1.gz) 165 Kb
  • Biological Unit Coordinates (1y13.pdb2.gz) 84 Kb
  • LPC: Ligand-Protein Contacts for 1Y13
  • CSU: Contacts of Structural Units for 1Y13
  • Likely Quarternary Molecular Structure file(s) for 1Y13
  • Structure Factors (621 Kb)
  • Retrieve 1Y13 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Y13 from S2C, [Save to disk]
  • Re-refined 1y13 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1Y13 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 1Y13
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1Y13, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1y13a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1y13b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1y13c_, region C [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1y13_B] [1y13] [1y13_A] [1y13_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 1Y13
  • Community annotation for 1Y13 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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