4ND4 Oxidoreductase date Oct 25, 2013
title Crystal Structure Of The Lactate Dehydrogenase From Cryptosp Parvum Complexed With Substrate (Pyruvic Acid) And Cofactor Nicotinamide Adenine Dinucleotide)
authors D.Chattopadhyay, W.J.Cook
compound source
Molecule: Lactate Dehydrogenase, Adjacent Gene Encodes Pred Malate Dehydrogenase;
Chain: A, B
Fragment: Unp Residues 17-337
Ec: 1.1.1.27
Engineered: Yes
Organism_scientific: Cryptosporidium Parvum
Organism_taxid: 353152
Strain: Iowa II
Gene: Cgd7_480, Ldh1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21a
symmetry Space Group: P 32 2 1
R_factor 0.201 R_Free 0.223
crystal
cell
length a length b length c angle alpha angle beta angle gamma
95.905 95.905 185.723 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand GOL, NAD, PYR enzyme Oxidoreductase E.C.1.1.1.27 BRENDA
note 4ND4 supersedes 2FM3
Gene CGD7
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceBiochemical and structural characterization of Cryptosporidium parvum Lactate dehydrogenase., Cook WJ, Senkovich O, Hernandez A, Speed H, Chattopadhyay D, Int J Biol Macromol. 2015 Mar;74:608-19. doi: 10.1016/j.ijbiomac.2014.12.019., Epub 2014 Dec 24. PMID:25542170
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (110 Kb) [Save to disk]
  • Biological Unit Coordinates (4nd4.pdb1.gz) 205 Kb
  • LPC: Ligand-Protein Contacts for 4ND4
  • CSU: Contacts of Structural Units for 4ND4
  • Structure Factors (440 Kb)
  • Retrieve 4ND4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4ND4 from S2C, [Save to disk]
  • Re-refined 4nd4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4ND4 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 4ND4
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4ND4, from MSDmotif at EBI
  • Fold representative 4nd4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4nd4_A] [4nd4] [4nd4_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4ND4
  • Community annotation for 4ND4 at PDBWiki (http://pdbwiki.org)

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