3E3Y Hydrolase Dna date Aug 08, 2008
title Q138f Hincii Bound To Gttaac And Cocrystallized With 5 Mm Ca2+
authors N.C.Horton, A.C.Babic, E.J.Little, V.M.Manohar
compound source
Molecule: Type-2 Restriction Enzyme Hindii
Chain: A, B
Synonym: R.Hindii, Type II Restriction Enzyme Hindii, Endonuclease Hindii;
Engineered: Yes
Mutation: Yes
Organism_scientific: Haemophilus Influenzae
Organism_taxid: 727
Gene: Hindiir, Hi0512
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: 5'- D(Dgpdcpdcpdgpdgpdtpdtpdapdapdcpdcpdgpdgpdc)- 3';
Chain: E, F
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.180 R_Free 0.234
length a length b length c angle alpha angle beta angle gamma
50.480 91.640 65.780 90.00 104.92 90.00
method X-Ray Diffractionresolution 2.13 Å
ligand CA, NA enzyme Hydrolase E.C. BRENDA
A, B
  • nuclease activity
  • endonuclease activity

  • Primary referenceDNA distortion and specificity in a sequence-specific endonuclease., Babic AC, Little EJ, Manohar VM, Bitinaite J, Horton NC, J Mol Biol. 2008 Oct 31;383(1):186-204. Epub 2008 Aug 22. PMID:18762194
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (105 Kb) [Save to disk]
  • Biological Unit Coordinates (3e3y.pdb1.gz) 99 Kb
  • LPC: Ligand-Protein Contacts for 3E3Y
  • CSU: Contacts of Structural Units for 3E3Y
  • Likely Quarternary Molecular Structure file(s) for 3E3Y
  • Structure Factors (257 Kb)
  • Retrieve 3E3Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3E3Y from S2C, [Save to disk]
  • Re-refined 3e3y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3E3Y 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 3E3Y
  • 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 3E3Y, from MSDmotif at EBI
  • Fold representative 3e3y from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3e3y_E] [3e3y_F] [3e3y_A] [3e3y_B] [3e3y]
  • SWISS-PROT database: [P44413]
  • Domain organization of [T2D2_HAEIN] by SWISSPFAM
  • Other resources with information on 3E3Y
  • Community annotation for 3E3Y 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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