3NDK	Transferase Dna	date	Jun 07, 2010
title	Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp Opposi
authors	M.Wang, J.Wang, W.H.Konigsberg
compound		source
Molecule: Dna Polymerase Chain: A Synonym: Gp43 Ec: 2.7.7.7 Engineered: Yes Mutation: Yes		Organism_scientific: Enterobacteria Phage Rb69 Organism_common: Bacteriophage Rb69 Organism_taxid: 12353 Gene: 43, Gp43 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet21b
Molecule: Dna (5'- D(Tpcpapgpgptpapapgpcpapgptpcpcpgpcpg)-3' Chain: T Engineered: Yes Other_details: Template Dna Strand		Synthetic: Yes
Molecule: Dna (5'-D(Gpcpgpgpapcptpgpcptptpap(D Chain: P Engineered: Yes Other_details: Primer Dna Strand		Synthetic: Yes
symmetry	Space Group: P 21 21 21	R_factor 0.187 R_Free 0.229
crystal cell	length a length b length c angle alpha angle beta angle gamma 75.006 120.015 130.781 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.00 Å
ligand	CA, DCP, DOC	enzyme	Transferase E.C.2.7.7.7 BRENDA
Gene Ontology	Chain Function Process Component A DNA-directed DNA polymerase ... nuclease activity exonuclease activity 3'-5' exonuclease activity
Primary reference	Variation in Mutation Rates Caused by RB69pol Fidelity Mutants Can Be Rationalized on the Basis of Their Kinetic Behavior and Crystal Structures., Xia S, Wang M, Lee HR, Sinha A, Blaha G, Christian T, Wang J, Konigsberg W, J Mol Biol. 2011 Jan 7. PMID:21216248

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (186 Kb) [Save to disk] Biological Unit Coordinates (3ndk.pdb1.gz) 179 Kb LPC: Ligand-Protein Contacts for 3NDK CSU: Contacts of Structural Units for 3NDK Structure Factors (1200 Kb) Retrieve 3NDK in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3NDK from S2C, [Save to disk] Re-refined 3ndk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3NDK 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 3NDK

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 3NDK, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3ndk_P] [3ndk] [3ndk_T] [3ndk_A] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 3NDK: [POLBc ] by SMART

Other resources with information on 3NDK

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

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