4YIH Hydrolase Hydrolase Inhibitor date Nov 20, 2013
title Crystal Structure Of Human Cytosolic 5'(3')-Deoxyribonucleot Complex With The Inhibitor Pb-Pvu
authors P.Pachl, P.Rezacova, J.Brynda
compound source
Molecule: 5'(3')-Deoxyribonucleotidase, Cytosolic Type
Chain: A, B
Fragment: Unp Residues 1-195
Synonym: Cytosolic 5',3'-Pyrimidine Nucleotidase,Deoxy-5'- Nucleotidase 1,Dnt-1;
Ec: 3.1.3.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nt5c, Dnt1, Umph2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.185 R_Free 0.228
length a length b length c angle alpha angle beta angle gamma
38.818 46.451 61.738 111.18 88.16 104.70
method X-Ray Diffractionresolution 1.82 Å
ligand 2O2, GOL, MG, PO4 enzyme Hydrolase E.C.3.1.3 BRENDA
A, B

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (141 Kb) [Save to disk]
  • Biological Unit Coordinates (4yih.pdb1.gz) 134 Kb
  • LPC: Ligand-Protein Contacts for 4YIH
  • CSU: Contacts of Structural Units for 4YIH
  • Structure Factors (469 Kb)
  • Retrieve 4YIH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YIH from S2C, [Save to disk]
  • Re-refined 4yih structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4YIH 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 4YIH
  • 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
  • Fold representative 4yih from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4yih_A] [4yih] [4yih_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4YIH
  • Community annotation for 4YIH at PDBWiki (http://pdbwiki.org)

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