3D4V	Hydrolase Dna	date	May 15, 2008
title	Crystal Structure Of An Alka Hostguest Complex N7methylguanine:Cytosine Base Pair
authors	S.Lee, B.R.Bowman, 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; Ec: 3.2.2.21 Engineered: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 562 Gene: Alka, Aida, B2068, Jw2053 Expression_system: Escherichia Coli Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet30
Molecule: 5'-D(Dgpdapdcpdapdtpdgpdap(Fmg)Pdtpdgp 3'; Chain: E, G Engineered: Yes		Synthetic: Yes
Molecule: 5'-D(Dgpdgpdcpdapdcpdtpdcpdapdtpdgpdtp Chain: F, H Engineered: Yes		Synthetic: Yes
symmetry	Space Group: P 1 21 1	R_factor 0.208 R_Free 0.275
crystal cell	length a length b length c angle alpha angle beta angle gamma 74.100 100.361 102.281 90.00 94.45 90.00
method	X-Ray Diffraction	resolution	2.90 Å
ligand	FMG	enzyme	Hydrolase E.C.3.2.2.21 BRENDA
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	Synthesis and structure of duplex DNA containing the genotoxic nucleobase lesion N7-methylguanine., Lee S, Bowman BR, Ueno Y, Wang S, Verdine GL, J Am Chem Soc. 2008 Sep 3;130(35):11570-1. Epub 2008 Aug 8. PMID:18686953

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (202 Kb) [Save to disk] Biological Unit Coordinates (3d4v.pdb1.gz) 196 Kb LPC: Ligand-Protein Contacts for 3D4V CSU: Contacts of Structural Units for 3D4V Likely Quarternary Molecular Structure file(s) for 3D4V Structure Factors (218 Kb) Retrieve 3D4V in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3D4V from S2C, [Save to disk] Re-refined 3d4v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3D4V 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 3D4V

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 3D motif for 3D4V, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3d4v_G] [3d4v_B] [3d4v_F] [3d4v_A] [3d4v_D] [3d4v] [3d4v_H] [3d4v_C] [3d4v_E] SWISS-PROT database: [P04395] Domain organization of [3MG2_ECOLI] by SWISSPFAM Domains found in 3D4V: [AlkA_N] [ENDO3c ] by SMART

Other resources with information on 3D4V

Community annotation for 3D4V at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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