3KD1	Transferase Dna	date	Oct 22, 2009
title	Closed Binary Complex Of An Rb69 Gp43 Fingers Domain Mutant With An Acyclic Gmp Terminated Primer Template Pair.
authors	K.E.Zahn, S.Doublie
compound		source
Molecule: Dna (5'- D(Cpgptpcptptpaptpgpapcpapgpcpcpgpcpg)-3' Chain: T Engineered: Yes		Synthetic: Yes Other_details: Oligonucleotide Was Chemically Synthesized
Molecule: Dna (5'-D(Gpcpgpgpcptpgptpcpaptpapap 3'); Chain: P Fragment: Acyclic Gmp Terminated Primer Dna Engineered: Yes		Synthetic: Yes Other_details: Oligonucleotide Was Chemically Synthesized
Molecule: Dna Polymerase Chain: E Fragment: Rb69 Gp43 Exo- Chimera Containing Elements From T Domain Of The Human Cytomegalovirus Dna Polymerase.; 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, Rb69 Gp43 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 De3 Expression_system_vector_type: Plasmid Expression_system_plasmid: Ppr-Iba1
symmetry	Space Group: P 21 21 21	R_factor 0.208 R_Free 0.248
crystal cell	length a length b length c angle alpha angle beta angle gamma 78.485 121.657 131.538 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.66 Å
ligand	4DG, MG	enzyme	Transferase E.C.2.7.7.7 BRENDA
Gene Ontology	Chain Function Process Component E DNA-directed DNA polymerase ... nuclease activity exonuclease activity 3'-5' exonuclease activity
Primary reference	Phosphonoformic acid inhibits viral replication by trapping the closed form of the DNA polymerase., Zahn KE, Tchesnokov EP, Gotte M, Doublie S, J Biol Chem. 2011 Jul 15;286(28):25246-55. doi: 10.1074/jbc.M111.248864. Epub, 2011 May 12. PMID:21566148

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (168 Kb) [Save to disk] Biological Unit Coordinates (3kd1.pdb1.gz) 161 Kb LPC: Ligand-Protein Contacts for 3KD1 CSU: Contacts of Structural Units for 3KD1 Structure Factors (1824 Kb) Retrieve 3KD1 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3KD1 from S2C, [Save to disk] Re-refined 3kd1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3KD1 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 3KD1

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 3KD1, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1m3kd1, region D:1-268 [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3kd1_P] [3kd1_E] [3kd1_T] [3kd1] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 3KD1: [POLBc ] by SMART

Other resources with information on 3KD1

Community annotation for 3KD1 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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