3QE9 Hydrolase Dna date Jan 20, 2011
title Crystal Structure Of Human Exonuclease 1 Exo1 (D173a) In Com Dna (Complex I)
authors J.Orans, E.A.Mcsweeney, R.R.Iyer, M.A.Hast, H.W.Hellinga, P.Modri L.S.Beese
compound source
Molecule: Exonuclease 1
Chain: Y, Z
Synonym: Hexo1, Exonuclease I, Hexoi
Ec: 3.1.-.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Exo1, Exoi, Hex1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Cpgpcptpapgptpcpgpapcpapt)
Chain: C, A
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'-D(Ptpcpgpapcptpapgpcpg)-3')
Chain: D, B
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 2
R_factor 0.215 R_Free 0.238
length a length b length c angle alpha angle beta angle gamma
92.504 95.467 99.777 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.51 Å
ligand CA, K enzyme Hydrolase E.C.3.1 BRENDA
Z, Y

Primary referenceStructures of human exonuclease 1 DNA complexes suggest a unified mechanism for nuclease family., Orans J, McSweeney EA, Iyer RR, Hast MA, Hellinga HW, Modrich P, Beese LS, Cell. 2011 Apr 15;145(2):212-23. PMID:21496642
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (140 Kb) [Save to disk]
  • Biological Unit Coordinates (3qe9.pdb1.gz) 69 Kb
  • Biological Unit Coordinates (3qe9.pdb2.gz) 69 Kb
  • LPC: Ligand-Protein Contacts for 3QE9
  • CSU: Contacts of Structural Units for 3QE9
  • Structure Factors (425 Kb)
  • Retrieve 3QE9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3QE9 from S2C, [Save to disk]
  • Re-refined 3qe9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3QE9 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 3QE9
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3QE9, from MSDmotif at EBI
  • Fold representative 3qe9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3qe9_A] [3qe9] [3qe9_Y] [3qe9_C] [3qe9_Z] [3qe9_B] [3qe9_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3QE9: [HhH2] [XPGI] [XPGN ] by SMART
  • Other resources with information on 3QE9
  • Community annotation for 3QE9 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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