5Y7Q Hydrolase Dna date Aug 17, 2017
title Crystal Structure Of Pafan1 Bound To 2nt 5'Flap Dna With Gap
authors H.Jin, Y.Cho
compound source
Molecule: Fanconi-Associated Nuclease 1 Homolog
Chain: A
Synonym: Pfan1
Ec: 3.1.4.1
Engineered: Yes
 Organism_scientific: Pseudomonas Aeruginosa (Strain Atcc 15 22644 Cip 104116 Jcm 14847 Lmg 12228 1c Prs 101
Organism_taxid: 208964
Strain: Atcc 15692 Dsm 22644 Cip 104116 Jcm 14847 L 1c Prs 101 Pao1;
Gene: Fan1, Pa1865
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Pgptptpgpgpgpaptptpg)-3')
Chain: D
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Tptpcpapcpapcpaptptpcpapa)
Chain: B
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Pgpapaptpgptpgptpgptpcptpcpapaptpcpcpc Tpt)-3');
Chain: C
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.193 R_Free 0.243
crystal
cell
length a length b length c angle alpha angle beta angle gamma
80.845 104.560 105.243 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand
enzyme Hydrolase E.C.3.1.4.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • nuclease activity
  • endonuclease activity
  • exonuclease activity
  • phosphodiesterase I activity...
  • 5'-3' exonuclease activity


    • Primary referenceStructural mechanism of DNA interstrand cross-link unhooking by the bacterial FAN1 nuclease., Jin H, Roy U, Lee G, Scharer OD, Cho Y, J Biol Chem. 2018 Apr 27;293(17):6482-6496. doi: 10.1074/jbc.RA118.002171. Epub, 2018 Mar 7. PMID:29514982
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (225 Kb) [Save to disk]
  • Biological Unit Coordinates (5y7q.pdb1.gz) 218 Kb
  • CSU: Contacts of Structural Units for 5Y7Q
  • Structure Factors (656 Kb)
  • Retrieve 5Y7Q in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5Y7Q from S2C, [Save to disk]
    • View 5Y7Q 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 5Y7Q
  • 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: [5y7q_A] [5y7q_C] [5y7q_D] [5y7q_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5Y7Q
  • Community annotation for 5Y7Q at PDBWiki (http://pdbwiki.org)

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