3Q8M Hydrolase Dna date Jan 06, 2011
title Crystal Structure Of Human Flap Endonuclease Fen1 (D181a) In With Substrate 5'-Flap Dna And K+
authors S.E.Tsutakawa, S.Classen, B.R.Chapados, A.Arvai, D.L.Finger, G.Gu C.G.Tomlinson, P.Thompson, A.H.Sarker, B.Shen, P.K.Cooper, J.A.G J.A.Tainer
compound source
Molecule: Flap Endonuclease 1
Chain: A, B
Fragment: D181a
Synonym: Fen-1, Dnase Iv, Flap Structure-Specific Endonucle Maturation Factor 1, Mf1, Hfen-1;
Ec: 3.1.-.-
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Fen1, Rad2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Rosetta2 De3 Plyss Cells
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet29b

Molecule: Dna (5'- D(Apcptpcptpgpcpcptpcpapapgpapcpgpgpt)-3'
Chain: D, G
Engineered: Yes
Other_details: Template Strand Of Dna Substrate
Synthetic: Yes
Other_details: Synthesized

Molecule: Dna (5'-D(Tptpgpapgpgpcpapgpapgpt)-3'
Chain: E, H
Engineered: Yes
Other_details: 5'-Flap Strand Of Dna Substrate
Synthetic: Yes
Other_details: Synthesized

Molecule: Dna (5'-D(Apcpcpgptpcpc)-3')
Chain: F, I
Engineered: Yes
Other_details: 3'-Flap Strand Of Dna Substrate
Synthetic: Yes
Other_details: Synthesized
symmetry Space Group: P 1 21 1
R_factor 0.217 R_Free 0.272
crystal
cell
length a length b length c angle alpha angle beta angle gamma
59.520 94.940 104.520 90.00 105.06 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand K enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceHuman Flap Endonuclease Structures, DNA Double-Base Flipping, and a Unified Understanding of the FEN1 Superfamily., Tsutakawa SE, Classen S, Chapados BR, Arvai AS, Finger LD, Guenther G, Tomlinson CG, Thompson P, Sarker AH, Shen B, Cooper PK, Grasby JA, Tainer JA, Cell. 2011 Apr 15;145(2):198-211. PMID:21496641
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (259 Kb) [Save to disk]
  • Biological Unit Coordinates (3q8m.pdb1.gz) 128 Kb
  • Biological Unit Coordinates (3q8m.pdb2.gz) 127 Kb
  • LPC: Ligand-Protein Contacts for 3Q8M
  • CSU: Contacts of Structural Units for 3Q8M
  • Structure Factors (380 Kb)
  • Retrieve 3Q8M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3Q8M from S2C, [Save to disk]
  • Re-refined 3q8m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3Q8M 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 3Q8M
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3Q8M, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3q8m_H] [3q8m] [3q8m_B] [3q8m_F] [3q8m_D] [3q8m_I] [3q8m_A] [3q8m_E] [3q8m_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3Q8M: [HhH2] [XPGI] [XPGN ] by SMART
    • Other resources with information on 3Q8M
  • Community annotation for 3Q8M at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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