5GKF Hydrolase Dna date Jul 04, 2016
title Structure Of Endoms-Dsdna1' Complex
authors S.Nakae, A.Hijikata, T.Tsuji, K.Yonezawa, K.Kouyama, K.Mayanagi, S Y.Ishino, T.Shirai
compound source
Molecule: Endonuclease Endoms
Chain: A, B
Synonym: Endonuclease Nucs
Ec: 3.1.-.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Thermococcus Kodakarensis Kod1
Organism_taxid: 69014
Strain: Kod1
Gene: Tk1898
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Cpgpcptpapcpaptpgptpcpgptp 3');
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Gpgpapcpgpapcptptpgptpapgp 3');
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 61 2 2
R_factor 0.171 R_Free 0.247
length a length b length c angle alpha angle beta angle gamma
92.440 92.440 404.320 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.80 Å
ligand MG, MPD enzyme Hydrolase E.C.3.1 BRENDA
A, B
  • single-stranded DNA endodeox...
  • nuclease activity
  • endonuclease activity

  • Primary referenceStructure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease., Nakae S, Hijikata A, Tsuji T, Yonezawa K, Kouyama KI, Mayanagi K, Ishino S, Ishino Y, Shirai T, Structure. 2016 Oct 17. pii: S0969-2126(16)30294-5. doi:, 10.1016/j.str.2016.09.005. PMID:27773688
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (109 Kb) [Save to disk]
  • Biological Unit Coordinates (5gkf.pdb1.gz) 104 Kb
  • LPC: Ligand-Protein Contacts for 5GKF
  • CSU: Contacts of Structural Units for 5GKF
  • Structure Factors (466 Kb)
  • Retrieve 5GKF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5GKF from S2C, [Save to disk]
  • Re-refined 5gkf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
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  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5gkf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5gkf] [5gkf_D] [5gkf_A] [5gkf_B] [5gkf_C]
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