5Y7G Hydrolase Dna date Aug 17, 2017
title Crystal Structure Of Pafan1 Bound To 1nt 5'Flap Dna With Gap
authors Y.Cho, H.Jin
compound source
Molecule: Fanconi-Associated Nuclease 1 Homolog
Chain: A, B, C
Synonym: Pfan1
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, F, H
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Pgpapaptpgptpgptpgptpcptpcpapaptpcpcpc Tpt)-3');
Chain: E, G, I
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Ptpgpapcpapcpapcpaptptpcpa
Chain: J, L, N
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.221 R_Free 0.280
length a length b length c angle alpha angle beta angle gamma
140.290 143.258 172.712 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.40 Å
ligand CA enzyme Hydrolase E.C. BRENDA
A, C, B
  • 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] (722 Kb) [Save to disk]
  • Biological Unit Coordinates (5y7g.pdb1.gz) 239 Kb
  • Biological Unit Coordinates (5y7g.pdb2.gz) 241 Kb
  • Biological Unit Coordinates (5y7g.pdb3.gz) 239 Kb
  • LPC: Ligand-Protein Contacts for 5Y7G
  • CSU: Contacts of Structural Units for 5Y7G
  • Structure Factors (1245 Kb)
  • Retrieve 5Y7G in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5Y7G from S2C, [Save to disk]
  • View 5Y7G 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 5Y7G
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5y7g from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5y7g_H] [5y7g_N] [5y7g_D] [5y7g_G] [5y7g_C] [5y7g_F] [5y7g_B] [5y7g_I] [5y7g_E] [5y7g_L] [5y7g_J] [5y7g_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5Y7G
  • Community annotation for 5Y7G at PDBWiki (http://pdbwiki.org)

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