4R8A Hydrolase Dna date Aug 30, 2014
title Crystal Structure Of Pafan1 - 5' Flap Dna Complex
authors Y.Cho, G.H.Gwon, Y.R.Kim
compound source
Molecule: Uncharacterized Protein
Chain: A, F
Synonym: Nuclease
Engineered: Yes
Organism_scientific: Pseudomonas Aeruginosa
Organism_taxid: 208964
Strain: Pao1
Gene: Pa1865
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Papcpcpapgpapcpapcpapcpapt 3');
Chain: B, G
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna

Molecule: Dna (5'-D(Pgptptpgpgpgpaptptpg)-3')
Chain: C, H
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna

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

Synthetic: Yes
Other_details: Synthetic Dna
symmetry Space Group: P 1 21 1
R_factor 0.196 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
76.581 106.663 142.180 90.00 89.97 90.00
method X-Ray Diffractionresolution 3.20 Å
Gene
Ontology
ChainFunctionProcessComponent
F, A
  • nuclease activity
  • endonuclease activity
  • exonuclease activity
  • phosphodiesterase I activity...
  • 5'-3' exonuclease activity


  • Primary referenceCrystal structure of a Fanconi anemia-associated nuclease homolog bound to 5' flap DNA: basis of interstrand cross-link repair by FAN1., Gwon GH, Kim Y, Liu Y, Watson AT, Jo A, Etheridge TJ, Yuan F, Zhang Y, Kim Y, Carr AM, Cho Y, Genes Dev. 2014 Oct 15;28(20):2276-90. doi: 10.1101/gad.248492.114. PMID:25319828
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (461 Kb) [Save to disk]
  • Biological Unit Coordinates (4r8a.pdb1.gz) 229 Kb
  • Biological Unit Coordinates (4r8a.pdb2.gz) 227 Kb
  • CSU: Contacts of Structural Units for 4R8A
  • Structure Factors (702 Kb)
  • Retrieve 4R8A in mmCIF format [Save to disk]
  • Re-refined 4r8a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4R8A 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 4R8A
  • 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
  • 3D motif for 4R8A, from MSDmotif at EBI
  • Fold representative 4r8a from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4r8a_B] [4r8a_H] [4r8a_A] [4r8a_C] [4r8a_G] [4r8a] [4r8a_I] [4r8a_D] [4r8a_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4R8A: [VRR_NUC ] by SMART
  • Other resources with information on 4R8A
  • Community annotation for 4R8A at PDBWiki (http://pdbwiki.org)

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