5V09 Hydrolase Dna date Feb 28, 2017
title Crystal Structure Of Human Exonuclease 1 Exo1 (D225a) In Com 5' Recessed-End Dna (Rvii)
authors Y.Shi, L.S.Beese
compound source
Molecule: Exonuclease 1
Chain: Z
Fragment: Unp Residues 1-352
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(Cpgpcptpapgptpcpgptpcpapt)
Chain: A
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 43 21 2
R_factor 0.218 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.904 73.904 180.081 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.75 Å
ligand MN, NA enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
Z


Primary referenceInterplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I., Shi Y, Hellinga HW, Beese LS, Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):6010-6015. doi:, 10.1073/pnas.1704845114. Epub 2017 May 22. PMID:28533382
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (150 Kb) [Save to disk]
  • Biological Unit Coordinates (5v09.pdb1.gz) 140 Kb
  • LPC: Ligand-Protein Contacts for 5V09
  • CSU: Contacts of Structural Units for 5V09
  • Structure Factors (125 Kb)
  • Retrieve 5V09 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5V09 from S2C, [Save to disk]
  • Re-refined 5v09 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5V09 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 5V09
  • 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 5v09 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5v09_B] [5v09_Z] [5v09_A] [5v09]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5V09
  • Community annotation for 5V09 at PDBWiki (http://pdbwiki.org)

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