4YKL Hydrolase Dna date Mar 04, 2015
title Hnt3 In Complex With Dna And Guanosine
authors A.Jacewicz, M.Chauleau, S.Shuman
compound source
Molecule: Aprataxin-Like Protein
Chain: B
Fragment: Unp Residues 33-232
Synonym: Hit Family Protein 3
Ec: 3.-.-.-
Engineered: Yes
Organism_scientific: Schizosaccharomyces Pombe (Strain 972 24843);
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: 972 Atcc 24843
Gene: Hnt3, Spcc18.09c
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b-His10-Smt3

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Chemical Synthesis
symmetry Space Group: P 3 2 1
R_factor 0.180 R_Free 0.240
length a length b length c angle alpha angle beta angle gamma
119.083 119.083 36.564 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.25 Å
ligand CL, GMP, GOL, ZN enzyme Hydrolase E.C.3 BRENDA
Primary referenceDNA3'pp5'G de-capping activity of aprataxin: effect of cap nucleoside analogs and structural basis for guanosine recognition., Chauleau M, Jacewicz A, Shuman S, Nucleic Acids Res. 2015 May 24. pii: gkv501. PMID:26007660
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (85 Kb) [Save to disk]
  • Biological Unit Coordinates (4ykl.pdb1.gz) 154 Kb
  • LPC: Ligand-Protein Contacts for 4YKL
  • CSU: Contacts of Structural Units for 4YKL
  • Structure Factors (149 Kb)
  • Retrieve 4YKL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YKL from S2C, [Save to disk]
  • Re-refined 4ykl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4YKL 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 4YKL
  • 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 4YKL, from MSDmotif at EBI
  • Fold representative 4ykl from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ykl_B] [4ykl_A] [4ykl]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4YKL
  • Community annotation for 4YKL at PDBWiki (http://pdbwiki.org)

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