5HP4 Hydrolase date Jan 20, 2016
title Crystal Structure Bacteriohage T5 D15 Flap Endonuclease (D15 Pseudo-Enzyme-Product Complex With Dna And Metal Ions
authors F.A.Almalki, J.Zhang, S.E.Sedelnikova, J.B.Rafferty, J.R.Sayers, P.A.Artymiuk
compound source
Molecule: Dna (5'- D(Gpaptpcptpaptpaptpgpcpcpaptpcpgpg)-3');
Chain: X
Engineered: Yes
Other_details: Oligonucleotide Forms Imperfect Helical Dupl Overhang When Annealed.;
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Exodeoxyribonuclease
Chain: A
Fragment: Unp Residues 20-291
Synonym: 5'-Exonuclease,T5fen
Ec: 3.1.11.3
Engineered: Yes
Mutation: Yes
Other_details: The Expressed Recombinant Corresponded To Re 291 Of The Protein With A D155k Substitution.

Organism_scientific: Escherichia Phage T5
Organism_taxid: 10726
Gene: D15
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: M72
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pjonex4 Derivative
symmetry Space Group: P 43 21 2
R_factor 0.158 R_Free 0.188
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.510 67.510 187.810 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.86 Å
ligand CA, GOL, K, NA enzyme Hydrolase E.C.3.1.11.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • nuclease activity
  • endonuclease activity
  • exonuclease activity
  • 5'-3' exonuclease activity
  • 5'-3' exodeoxyribonuclease a...


  • Primary referenceDirect observation of DNA threading in flap endonuclease complexes., AlMalki FA, Flemming CS, Zhang J, Feng M, Sedelnikova SE, Ceska T, Rafferty JB, Sayers JR, Artymiuk PJ, Nat Struct Mol Biol. 2016 Jun 6. doi: 10.1038/nsmb.3241. PMID:27273516
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (113 Kb) [Save to disk]
  • Biological Unit Coordinates (5hp4.pdb1.gz) 136 Kb
  • LPC: Ligand-Protein Contacts for 5HP4
  • CSU: Contacts of Structural Units for 5HP4
  • Structure Factors (2541 Kb)
  • Retrieve 5HP4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5HP4 from S2C, [Save to disk]
  • Re-refined 5hp4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5HP4 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 5HP4
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5hp4_A] [5hp4_X] [5hp4]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5HP4: [53EXOc] [HhH2 ] by SMART
  • Other resources with information on 5HP4
  • Community annotation for 5HP4 at PDBWiki (http://pdbwiki.org)

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