2VGB Transferase date Nov 12, 2007
title Human Erythrocyte Pyruvate Kinase
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
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 0.227 R_Free 0.271
crystal
cell
length a length b length c angle alpha angle beta angle gamma
74.413 172.058 85.512 90.00 92.46 90.00
method X-Ray Diffractionresolution 2.73 Å
ligand FBP, K, MN, PGA enzyme Transferase E.C.2.7.1.40 BRENDA
note 2VGB supersedes 1LIU
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] (319 Kb) [Save to disk]
  • Biological Unit Coordinates (2vgb.pdb1.gz) 309 Kb
  • LPC: Ligand-Protein Contacts for 2VGB
  • CSU: Contacts of Structural Units for 2VGB
  • Likely Quarternary Molecular Structure file(s) for 2VGB
  • Structure Factors (451 Kb)
  • Retrieve 2VGB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VGB from S2C, [Save to disk]
  • Re-refined 2vgb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VGB 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 2VGB
  • 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 2VGB, from MSDmotif at EBI
  • Fold representative 2vgb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vgb_C] [2vgb_D] [2vgb_B] [2vgb] [2vgb_A]
  • SWISS-PROT database: [P30613]
  • Domain organization of [KPYR_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 2VGB with the sequences similar proteins can be viewed for 2VGB'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 2VGB
  • Community annotation for 2VGB 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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