3CWT Hydrolase Dna date Apr 22, 2008
title Crystal Structure Of An Alka Hostguest Complex 2'-Fluoro-2' Deoxyinosine:Adenine Base Pair
authors B.R.Bowman, S.Lee, S.Wang, G.L.Verdine
compound source
Molecule: Dna-3-Methyladenine Glycosylase 2
Chain: A, B, C, D
Synonym: Dna-3-Methyladenine Glycosylase II, 3-Methyladenin Glycosylase II, Inducible, Tag II, Dna-3-Methyladenine Glyc II;
Engineered: Yes
Organism_scientific: Escherichia Coli
Gene: Alka, Aida
Expression_system: Escherichia Coli
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30

Molecule: Dna (5'-D(Dgpdapdcpdapdtpdgpdap(2fi) Pdtpdgpdcpdc)-3');
Chain: E, G
Engineered: Yes
Other_details: 2'-Fluoro-2'-Deoxyinosine Containing Dna

Synthetic: Yes

Molecule: Dna (5'-D(Dgpdgpdcpdapdapdtpdcpdapdtpdg 3');
Chain: F, H
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.239 R_Free 0.280
length a length b length c angle alpha angle beta angle gamma
75.748 101.478 103.113 90.00 93.72 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand 2FI enzyme Hydrolase E.C. BRENDA
A, D, C, B

Primary referenceStructure of the E. coli DNA glycosylase AlkA bound to the ends of duplex DNA: a system for the structure determination of lesion-containing DNA., Bowman BR, Lee S, Wang S, Verdine GL, Structure. 2008 Aug 6;16(8):1166-74. PMID:18682218
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (205 Kb) [Save to disk]
  • Biological Unit Coordinates (3cwt.pdb1.gz) 201 Kb
  • LPC: Ligand-Protein Contacts for 3CWT
  • CSU: Contacts of Structural Units for 3CWT
  • Likely Quarternary Molecular Structure file(s) for 3CWT
  • Structure Factors (667 Kb)
  • Retrieve 3CWT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3CWT from S2C, [Save to disk]
  • Re-refined 3cwt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3CWT 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 3CWT
  • 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 3CWT, from MSDmotif at EBI
  • Fold representative 3cwt from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3cwt] [3cwt_G] [3cwt_F] [3cwt_B] [3cwt_E] [3cwt_D] [3cwt_H] [3cwt_A] [3cwt_C]
  • SWISS-PROT database: [P04395]
  • Domain organization of [3MG2_ECOLI] by SWISSPFAM
  • Domains found in 3CWT: [AlkA_N] [ENDO3c ] by SMART
  • Other resources with information on 3CWT
  • Community annotation for 3CWT 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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