3C2K	Transferase Dna	date	Jan 25, 2008
title	Dna Polymerase Beta With A Gapped Dna Substrate And Dumpnpp Manganese In The Active Site
authors	V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, S.H.Wilson
compound		source
Molecule: Dna (5'- D(Dcpdcpdgpdapdcpdapdgpdcpdgpdcpdapdtpdcpdap 3'); Chain: T Engineered: Yes		Synthetic: Yes
Molecule: Dna (5'-D(Dgpdcpdtpdgpdapdtpdgpdcpdgpdc Chain: P Engineered: Yes		Synthetic: Yes
Molecule: Dna (5'-D(Pdgpdtpdcpdgpdg)-3') Chain: D Engineered: Yes		Synthetic: Yes
Molecule: Dna Polymerase Beta Chain: A Ec: 2.7.7.7, 4.2.99.- Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Gene: Polb Expression_system: Escherichia Coli
symmetry	Space Group: P 1 21 1	R_factor 0.210 R_Free 0.278
crystal cell	length a length b length c angle alpha angle beta angle gamma 50.790 80.680 55.060 90.00 108.38 90.00
method	X-Ray Diffraction	resolution	2.40 Å
ligand	CL, DUP, MN, NA	enzyme	Transferase E.C.2.7.7.7 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation., Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson SH, Mol Cell. 2008 May 9;30(3):315-24. PMID:18471977

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (75 Kb) [Save to disk] Biological Unit Coordinates (3c2k.pdb1.gz) 70 Kb LPC: Ligand-Protein Contacts for 3C2K CSU: Contacts of Structural Units for 3C2K Likely Quarternary Molecular Structure file(s) for 3C2K Structure Factors (129 Kb) Retrieve 3C2K in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3C2K from S2C, [Save to disk] Re-refined 3c2k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3C2K 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 3C2K

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 3C2K, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3c2k_D] [3c2k_P] [3c2k_T] [3c2k] [3c2k_A] SWISS-PROT database: [P06746] Domain organization of [DPOLB_HUMAN] by SWISSPFAM Domains found in 3C2K: [HhH1] [POLXc ] by SMART

Other resources with information on 3C2K

Community annotation for 3C2K at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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