2VGI Transferase date Nov 13, 2007
title Human Erythrocyte Pyruvate Kinase: R486w Mutant
authors G.Valentini, L.Chiarelli, R.Fortin, M.Dolzan, A.Galizzi, D.J.Abra C.Wang, P.Bianchi, A.Zanella, A.Mattevi
compound source
Molecule: Pyruvate Kinase Isozymes Rl
Chain: A, B, C, D
Fragment: Residues 47-574
Synonym: R-Typel-Type Pyruvate Kinase, Red Cellliver Pyru Kinase, Pyruvate Kinase 1, Pyruvate Kinase;
Ec: 2.7.1.40
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
symmetry Space Group: P 1 21 1
R_factor 0.257 R_Free 0.311
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.705 171.164 85.050 90.00 91.61 90.00
method X-Ray Diffractionresolution 2.87 Å
ligand FBP, K, MN, PGA enzyme Transferase E.C.2.7.1.40 BRENDA
note 2VGI supersedes 1LIX
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructure and function of human erythrocyte pyruvate kinase. Molecular basis of nonspherocytic hemolytic anemia., Valentini G, Chiarelli LR, Fortin R, Dolzan M, Galizzi A, Abraham DJ, Wang C, Bianchi P, Zanella A, Mattevi A, J Biol Chem. 2002 Jun 28;277(26):23807-14. Epub 2002 Apr 17. PMID:11960989
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (275 Kb) [Save to disk]
  • Biological Unit Coordinates (2vgi.pdb1.gz) 264 Kb
  • LPC: Ligand-Protein Contacts for 2VGI
  • CSU: Contacts of Structural Units for 2VGI
  • Likely Quarternary Molecular Structure file(s) for 2VGI
  • Structure Factors (343 Kb)
  • Retrieve 2VGI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VGI from S2C, [Save to disk]
  • Re-refined 2vgi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VGI 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 2VGI
  • 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 2VGI, from MSDmotif at EBI
  • Fold representative 2vgi from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vgi] [2vgi_D] [2vgi_C] [2vgi_A] [2vgi_B]
  • SWISS-PROT database: [P30613]
  • Domain organization of [KPYR_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 2VGI with the sequences similar proteins can be viewed for 2VGI's classification [KPYR_HUMAN] 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 [KPYR_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2VGI
  • Community annotation for 2VGI 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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