5HNK Hydrolase date Jan 18, 2016
title Crystal Structure Of T5fen In Complex Intact Substrate And M
authors F.A.Almalki, M.Feng, J.Zhang, S.E.Sedelnikova, J.B.Rafferty, J.R. P.J.Artymiuk
compound source
Molecule: Dna (5'-D(Apapapapgpcpgptpapcpgpc)-3'
Chain: X, Y
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Exodeoxyribonuclease
Chain: A, B
Fragment: Unp Residues 20-291
Synonym: 5'-Exonuclease,T5fen, D15 Exonuclease
Ec: 3.1.11.3
Engineered: Yes
Other_details: Corresponds To Residues 20-291 Of Uniprot P0 With Mutation D153k

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
symmetry Space Group: P 21 21 21
R_factor 0.183 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.720 109.940 127.340 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.22 Å
ligand GOL, K, MG enzyme Hydrolase E.C.3.1.11.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • nuclease activity
  • endonuclease activity
  • exonuclease activity
  • 5'-3' exonuclease activity


  • 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] (214 Kb) [Save to disk]
  • Biological Unit Coordinates (5hnk.pdb1.gz) 116 Kb
  • Biological Unit Coordinates (5hnk.pdb2.gz) 116 Kb
  • LPC: Ligand-Protein Contacts for 5HNK
  • CSU: Contacts of Structural Units for 5HNK
  • Structure Factors (2076 Kb)
  • Retrieve 5HNK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5HNK from S2C, [Save to disk]
  • Re-refined 5hnk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5HNK 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 5HNK
  • 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 5hnk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5hnk_X] [5hnk] [5hnk_B] [5hnk_Y] [5hnk_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5HNK: [53EXOc] [HhH2 ] by SMART
  • Other resources with information on 5HNK
  • Community annotation for 5HNK at PDBWiki (http://pdbwiki.org)

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