2I7D Hydrolase date Aug 30, 2006
title Structure Of Human Cytosolic Deoxyribonucleotidase In Complex With Deoxyuridine, Alf4 And Mg2+
authors A.Rinaldo-Matthis, K.Wallden, P.Nordlund
compound source
Molecule: 5'(3')-Deoxyribonucleotidase, Cytosolic Type
Chain: A, B
Fragment: Residues 3-195
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
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.166 R_Free 0.196
length a length b length c angle alpha angle beta angle gamma
39.623 47.153 62.384 68.92 81.69 74.99
method X-Ray Diffractionresolution 1.20 Å
ligand ALF, DUR, MG enzyme Hydrolase E.C.3.1.3 BRENDA
note 2I7D is a representative structure
A, B

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (158 Kb) [Save to disk]
  • Biological Unit Coordinates (2i7d.pdb1.gz) 154 Kb
  • LPC: Ligand-Protein Contacts for 2I7D
  • CSU: Contacts of Structural Units for 2I7D
  • Likely Quarternary Molecular Structure file(s) for 2I7D
  • Structure Factors (852 Kb)
  • Retrieve 2I7D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2I7D from S2C, [Save to disk]
  • Re-refined 2i7d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2I7D 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 2I7D
  • 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 2I7D, from MSDmotif at EBI
  • Fold representative 2i7d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2i7d_B] [2i7d] [2i7d_A]
  • SWISS-PROT database: [Q8TCD5]
  • Domain organization of [NT5C_HUMAN] by SWISSPFAM
  • Other resources with information on 2I7D
  • Community annotation for 2I7D 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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