4KLD Transferase, Lyase Dna date May 07, 2013
title Dna Polymerase Beta Matched Substrate Complex With Ca2+, 0 S
authors B.D.Freudenthal, W.A.Beard, D.D.Shock, S.H.Wilson
compound source
Molecule: 5'-D(Cpcpgpapcpgpgpcpgpcpaptpcpapg
Chain: T
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Gpcptpgpaptpgpcpgpc)-3'
Chain: P
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Pgptpcpgpg)-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
Organism_taxid: 9606
Gene: Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Tap56
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pwl11
symmetry Space Group: P 1 21 1
R_factor 0.197 R_Free 0.251
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.800 80.400 55.500 90.00 107.90 90.00
method X-Ray Diffractionresolution 1.92 Å
ligand CA, CL, DCP, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceObserving a DNA polymerase choose right from wrong., Freudenthal BD, Beard WA, Shock DD, Wilson SH, Cell. 2013 Jul 3;154(1):157-68. doi: 10.1016/j.cell.2013.05.048. PMID:23827680
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (4kld.pdb1.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 4KLD
  • CSU: Contacts of Structural Units for 4KLD
  • Structure Factors (305 Kb)
  • Retrieve 4KLD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4KLD from S2C, [Save to disk]
  • Re-refined 4kld structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4KLD 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 4KLD
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4KLD, from MSDmotif at EBI
  • Fold representative 4kld from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4kld] [4kld_A] [4kld_D] [4kld_T] [4kld_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4KLD: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4KLD
  • Community annotation for 4KLD at PDBWiki (http://pdbwiki.org)

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