4IP7 Transferase date Jan 09, 2013
title Structure Of The S12d Variant Of Human Liver Pyruvate Kinase Complex With Citrate And Fbp.
authors T.Holyoak, A.W.Fenton
compound source
Molecule: Pyruvate Kinase Isozymes L
Chain: A, B, C, D
Fragment: Liver Isozyme
Synonym: Pyruvate Kinase 1, L-Type Pyruvate Kinase, Liver P Kinase;
Ec: 2.7.1.40
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pk1, Pkl, Pklr
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Ff50
Expression_system_vector_type: Plasmid
symmetry Space Group: P 1 21 1
R_factor 0.187 R_Free 0.226
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.140 205.078 83.910 90.00 92.15 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand 1PE, ADN, EDO, FBP, FLC, MN, NA, PEG enzyme Transferase E.C.2.7.1.40 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceEnergetic Coupling between an Oxidizable Cysteine and the Phosphorylatable N-Terminus of Human Liver Pyruvate Kinase., Holyoak T, Zhang B, Deng J, Tang Q, Prasannan CB, Fenton AW, Biochemistry. 2013 Jan 22;52(3):466-76. doi: 10.1021/bi301341r. Epub 2013 Jan 11. PMID:23270483
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (699 Kb) [Save to disk]
  • Biological Unit Coordinates (4ip7.pdb1.gz) 685 Kb
  • LPC: Ligand-Protein Contacts for 4IP7
  • CSU: Contacts of Structural Units for 4IP7
  • Structure Factors (3594 Kb)
  • Retrieve 4IP7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4IP7 from S2C, [Save to disk]
  • Re-refined 4ip7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4IP7 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 4IP7
  • 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 4IP7, from MSDmotif at EBI
  • Fold representative 4ip7 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ip7_A] [4ip7_C] [4ip7_D] [4ip7_B] [4ip7]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 4IP7 with the sequences similar proteins can be viewed for 4IP7's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 4IP7
  • Community annotation for 4IP7 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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