5K97 Hydrolase Dna date May 31, 2016
title Flap Endonuclease 1 (Fen1) D233n With Cleaved Product Fragme Sm3+
authors S.E.Tsutakawa, A.S.Arvai, J.A.Tainer
compound source
Molecule: Flap Endonuclease 1
Chain: A
Synonym: Fen-1,Dnase Iv,Flap Structure-Specific Endonucleas Maturation Factor 1,Hfen-1;
Ec: 3.1.-.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fen1, Rad2
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Dna Oligonucleotide Synthesis

Molecule: Dna (5'-D(Ptpgpapgpgpcpapgpapgpt)-3')
Chain: E
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Dna Oligonucleotide Synthesis

Molecule: Dna (5'-D(Apcpcpgptpcpc)-3')
Chain: F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Dna Oligonucleotide Synthesis

Molecule: Dna (5'-D(Ptpt)-3')
Chain: G
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Dna Oligonucleotide Synthesis
symmetry Space Group: P 31 2 1
R_factor 0.182 R_Free 0.219
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.236 105.236 104.548 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.10 Å
ligand EDO, K, SM enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referencePhosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability., Tsutakawa SE, Thompson MJ, Arvai AS, Neil AJ, Shaw SJ, Algasaier SI, Kim JC, Finger LD, Jardine E, Gotham VJB, Sarker AH, Her MZ, Rashid F, Hamdan SM, Mirkin SM, Grasby JA, Tainer JA, Nat Commun. 2017 Jun 27;8:15855. doi: 10.1038/ncomms15855. PMID:28653660
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (153 Kb) [Save to disk]
  • Biological Unit Coordinates (5k97.pdb1.gz) 146 Kb
  • LPC: Ligand-Protein Contacts for 5K97
  • CSU: Contacts of Structural Units for 5K97
  • Structure Factors (412 Kb)
  • Retrieve 5K97 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5K97 from S2C, [Save to disk]
  • Re-refined 5k97 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5K97 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 5K97
  • 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: [5k97_G] [5k97_D] [5k97_A] [5k97_E] [5k97_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5K97
  • Community annotation for 5K97 at PDBWiki (http://pdbwiki.org)

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