6G2N Hydrolase date Mar 23, 2018
title Crystal Structure Of Human Cytosolic 5'(3')-Deoxyribonucleot Complex With The Inhibitor Pb-Pau
authors P.Pachl, P.Rezacova, J.Brynda
compound source
Molecule: 5'(3')-Deoxyribonucleotidase, Cytosolic Type
Chain: A, B
Synonym: Cytosolic 5',3'-Pyrimidine Nucleotidase,Deoxy-5'- Nucleotidase 1,Dnt-1;
Ec: 3.1.3.-
Engineered: Yes
Other_details: Cme Is Beta-Mercapto Ethanol Covalently Boun Cystein Residue
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nt5c, Dnt1, Umph2
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
symmetry Space Group: P 1
R_factor 0.151 R_Free 0.192
crystal
cell
length a length b length c angle alpha angle beta angle gamma
38.877 47.231 61.795 67.86 88.69 77.37
method X-Ray Diffractionresolution 1.40 Å
ligand CME, MG, O84 enzyme Hydrolase E.C.3.1.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (146 Kb) [Save to disk]
  • Biological Unit Coordinates (6g2n.pdb1.gz) 140 Kb
  • LPC: Ligand-Protein Contacts for 6G2N
  • CSU: Contacts of Structural Units for 6G2N
  • Structure Factors (1705 Kb)
  • Retrieve 6G2N in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6G2N from S2C, [Save to disk]
    • View 6G2N 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 6G2N
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6g2n_B] [6g2n_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6G2N
  • Community annotation for 6G2N at PDBWiki (http://pdbwiki.org)

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