5CL4 Hydrolase Dna date Jul 16, 2015
title Alkylpurine Dna Glycosylase Alkd Bound To Dna Containing A 3 Methyladenine Analog Or Dna Containing An Abasic Site And A Nucleobase (71% Substrate29% Product At 24 Hours)
authors E.A.Mullins, B.F.Eichman
compound source
Molecule: Alkd
Chain: A
Ec: 3.2.2.-
Engineered: Yes
Organism_scientific: Bacillus Cereus
Organism_taxid: 1396
Atcc: 14579
Gene: Ike_03968
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Hms174
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbg103

Molecule: Dna (5'-D(Cpcpcpgpap(Dzm)Papgptpcpcpg
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.153 R_Free 0.196
crystal
cell
length a length b length c angle alpha angle beta angle gamma
38.247 93.558 47.976 90.00 112.74 90.00
method X-Ray Diffractionresolution 1.87 Å
ligand 54K, DZM, ORP enzyme Hydrolase E.C.3.2.2 BRENDA
Gene IKE
Primary referenceThe DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions., Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS, Igarashi Y, Eichman BF, Nature. 2015 Nov 12;527(7577):254-8. doi: 10.1038/nature15728. Epub 2015 Oct 28. PMID:26524531
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (115 Kb) [Save to disk]
  • Biological Unit Coordinates (5cl4.pdb1.gz) 108 Kb
  • LPC: Ligand-Protein Contacts for 5CL4
  • CSU: Contacts of Structural Units for 5CL4
  • Structure Factors (184 Kb)
  • Retrieve 5CL4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5CL4 from S2C, [Save to disk]
  • Re-refined 5cl4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5CL4 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 5CL4
  • 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
  • Fold representative 5cl4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5cl4] [5cl4_B] [5cl4_C] [5cl4_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5CL4
  • Community annotation for 5CL4 at PDBWiki (http://pdbwiki.org)

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