3C2K Transferase Dna date Jan 25, 2008
title Dna Polymerase Beta With A Gapped Dna Substrate And Dumpnpp With 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 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

Molecule: Dna (5'- D(Dcpdcpdgpdapdcpdapdgpdcpdgpdcpdapdtpdcpdap Dgpdc)-3');
Chain: T
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'- D(Dgpdcpdtpdgpdapdtpdgpdcpdgpdc)-3');
Chain: P
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'-D(Pdgpdtpdcpdgpdg)-3')
Chain: D
Engineered: Yes

Synthetic: Yes
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 Diffractionresolution 2.40 Å
ligand CL, DUP, MN, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructures 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] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (3c2k.pdb1.gz) 72 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
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3C2K, from MSDmotif at EBI
  • Fold representative 3c2k from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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