3JPN	Transferase Dna	date	Sep 04, 2009
title	Ternary Complex Of Dna Polymerase Beta With A Dideoxy Termin Primer And 2'-Deoxyguanosine 5'-Beta, Gamma-Dichloro Methyl Triphosphate
authors	V.K.Batra, J.Upton, B.Kashmerov, W.A.Beard, S.H.Wilson, M.F.Goodm C.E.Mckenna
compound		source
Molecule: Dna Polymerase Beta Chain: A Ec: 2.7.7.7 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Polb Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: 5'-D(Pgptpcpgpg)-3' Chain: D Engineered: Yes		Synthetic: Yes Other_details: Synthetic Oligonucleotide
Molecule: 5'-D(Gpcptpgpaptpgpcpgp(Doc))-3' Chain: P Engineered: Yes		Synthetic: Yes Other_details: Synthetic Oligonucleotide
Molecule: 5'-D(Cpcpgpapcpcpgpcpgpcpaptpcpapg Chain: T Engineered: Yes		Synthetic: Yes Other_details: Synthetic Oligonucleotide
symmetry	Space Group: P 1 21 1	R_factor 0.190 R_Free 0.242
crystal cell	length a length b length c angle alpha angle beta angle gamma 50.650 80.110 55.480 90.00 107.93 90.00
method	X-Ray Diffraction	resolution	2.15 Å
ligand	CL, DOC, G2C, MG	enzyme	Transferase E.C.2.7.7.7 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Halogenated beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary Complexes with DNA Polymerase beta: Structural Evidence for Stereospecific Binding of the Fluoromethylene Analogues., Batra VK, Pedersen LC, Beard WA, Wilson SH, Kashemirov BA, Upton TG, Goodman MF, McKenna CE, J Am Chem Soc. 2010 May 13. PMID:20465217

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk] Biological Unit Coordinates (3jpn.pdb1.gz) 73 Kb LPC: Ligand-Protein Contacts for 3JPN CSU: Contacts of Structural Units for 3JPN Structure Factors (181 Kb) Retrieve 3JPN in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3JPN from S2C, [Save to disk] Re-refined 3jpn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3JPN 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 3JPN

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 3JPN, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3jpn_T] [3jpn] [3jpn_P] [3jpn_A] [3jpn_D] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 3JPN: [HhH1] [POLXc ] by SMART

Other resources with information on 3JPN

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

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