5KK5 Hydrolase Dna Rna date Jun 21, 2016
title Ascpf1(E993a)-Crrna-Dna Ternary Complex
authors P.Gao, H.Yang, K.R.Rajashankar, Z.Huang, D.J.Patel
compound source
Molecule: Crispr-Associated Endonuclease Cpf1
Chain: A
Synonym: Ascpf1
Ec: 3.1.-.-
Engineered: Yes
Mutation: Yes
 Organism_scientific: Acidaminococcus Sp. (Strain Bv3l6)
Organism_taxid: 1111120
Strain: Bv3l6
Gene: Cpf1, Hmpref1246_0236
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)-Ril

Molecule: Rna (40-Mer)
Chain: B
Engineered: Yes
Synthetic: Yes
Organism_scientific: Acidaminococcus Sp. Bv3l6
Organism_taxid: 1111120

Molecule: Dna (28-Mer)
Chain: C
Engineered: Yes
Synthetic: Yes
Organism_scientific: Acidaminococcus Sp. Bv3l6
Organism_taxid: 1111120

Molecule: Dna (8-Mer)
Chain: D
Engineered: Yes
Synthetic: Yes
Organism_scientific: Acidaminococcus Sp. Bv3l6
Organism_taxid: 1111120
symmetry Space Group: P 41 21 2
R_factor 0.216 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
195.737 195.737 125.206 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.29 Å
ligand
enzyme Hydrolase E.C.3.1 BRENDA
Gene HMPREF1246
Gene
Ontology
ChainFunctionProcessComponent
A
  • nuclease activity
  • endonuclease activity
  • deoxyribonuclease I activity...
  • Bacillus subtilis ribonuclea...


    • Primary referenceType V CRISPR-Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition., Gao P, Yang H, Rajashankar KR, Huang Z, Patel DJ, Cell Res. 2016 Aug;26(8):901-13. doi: 10.1038/cr.2016.88. Epub 2016 Jul 22. PMID:27444870
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (488 Kb) [Save to disk]
  • Biological Unit Coordinates (5kk5.pdb1.gz) 479 Kb
  • CSU: Contacts of Structural Units for 5KK5
  • Structure Factors (330 Kb)
  • Retrieve 5KK5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5KK5 from S2C, [Save to disk]
  • Re-refined 5kk5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5KK5 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 5KK5
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5kk5_B] [5kk5_D] [5kk5] [5kk5_A] [5kk5_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5KK5
  • Community annotation for 5KK5 at PDBWiki (http://pdbwiki.org)

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science