2JCM Hydrolase date Dec 27, 2006
title Crystal Structure Of Human Cytosolic 5'-Nucleotidase II In Complex With Beryllium Trifluoride
authors K.Wallden, P.Stenmark, C.Arrowsmith, H.Berglund, R.Busam, R.Colli A.Edwards, M.Ehn, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, B.M.Hallberg, L.Holmberg Schiavone, M.Hogbom, T.Karlberg, T.Kot A.Magnusdottir, P.Nilsson-Ehle, T.Nyman, D.Ogg, C.Persson, J.Sag M.Sundstrom, J.Uppenberg, A.G.Thorsell, S.Van Den Berg, P.Loppn J.Weigelt, M.Welin, P.Nordlund
compound source
Molecule: Cytosolic Purine 5'-Nucleotidase
Chain: A
Fragment: Residues 1-536
Synonym: 5'-Nucleotidase Cytosolic II, Cytosolic 5'-Nucleot
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta2(De)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: P28a-Lic
symmetry Space Group: I 2 2 2
R_factor 0.210 R_Free 0.266
length a length b length c angle alpha angle beta angle gamma
91.480 128.260 131.010 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand BFD, MG, SO4, UNX enzyme Hydrolase E.C. BRENDA
  • 5'-nucleotidase activity

  • Primary referenceCrystal structure of human cytosolic 5'-nucleotidase II: insights into allosteric regulation and substrate recognition., Wallden K, Stenmark P, Nyman T, Flodin S, Graslund S, Loppnau P, Bianchi V, Nordlund P, J Biol Chem. 2007 Jun 15;282(24):17828-36. Epub 2007 Apr 3. PMID:17405878
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (91 Kb) [Save to disk]
  • Biological Unit Coordinates (2jcm.pdb1.gz) 165 Kb
  • LPC: Ligand-Protein Contacts for 2JCM
  • CSU: Contacts of Structural Units for 2JCM
  • Likely Quarternary Molecular Structure file(s) for 2JCM
  • Structure Factors (601 Kb)
  • Retrieve 2JCM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2JCM from S2C, [Save to disk]
  • Re-refined 2jcm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2JCM 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 2JCM
  • 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 2JCM, from MSDmotif at EBI
  • Fold representative 2jcm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2jcm] [2jcm_A]
  • SWISS-PROT database: [P49902]
  • Domain organization of [5NTC_HUMAN] by SWISSPFAM
  • Other resources with information on 2JCM
  • Community annotation for 2JCM 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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