3C5G Transferase Dna, Lyase Dna date Jan 31, 2008
title Structure Of A Ternary Complex Of The R517k Pol Lambda Mutan
authors M.Garcia-Diaz, K.Bebenek, M.C.Foley, L.C.Pedersen, T.Schlick, T.A
compound source
Molecule: Dna Polymerase Lambda
Chain: A, B
Fragment: Dna Binding Region
Synonym: Pol Lambda, Dna Polymerase Kappa, Dna Polymerase B Beta2;
Ec: 2.7.7.7, 4.2.99.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Gene: Poll
Expression_system: Escherichia Coli
Expression_system_strain: Bl21-Codonplus-Ril

Molecule: Dna (5'-D(Dcpdgpdgpdcpdapdapdtpdapdcpdt
Chain: T, U
Engineered: Yes
Other_details: Template

Synthetic: Yes

Molecule: Dna (5'-D(Dcpdapdgpdtpdap(2dt))-3')
Chain: P, Q
Engineered: Yes
Other_details: Primer

Synthetic: Yes

Molecule: Dna (5'-D(Pdgpdcpdcpdg)-3')
Chain: D, E
Engineered: Yes
Other_details: Downstream Primer

Synthetic: Yes
symmetry Space Group: P 21 21 2
R_factor 0.201 R_Free 0.236
crystal
cell
length a length b length c angle alpha angle beta angle gamma
94.335 150.819 85.822 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand 2DT, D3T, EDO, MG, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceSubstrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda., Bebenek K, Garcia-Diaz M, Foley MC, Pedersen LC, Schlick T, Kunkel TA, EMBO Rep. 2008 May;9(5):459-64. Epub 2008 Mar 28. PMID:18369368
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (148 Kb) [Save to disk]
  • Biological Unit Coordinates (3c5g.pdb1.gz) 70 Kb
  • Biological Unit Coordinates (3c5g.pdb2.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 3C5G
  • CSU: Contacts of Structural Units for 3C5G
  • Likely Quarternary Molecular Structure file(s) for 3C5G
  • Structure Factors (817 Kb)
  • Retrieve 3C5G in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3C5G from S2C, [Save to disk]
  • Re-refined 3c5g structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3C5G 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 3C5G
  • 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 3C5G, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3c5g_T] [3c5g_A] [3c5g_U] [3c5g_P] [3c5g_Q] [3c5g_D] [3c5g] [3c5g_E] [3c5g_B]
  • SWISS-PROT database: [Q9UGP5]
  • Domain organization of [DPOLL_HUMAN] by SWISSPFAM
  • Domains found in 3C5G: [HhH1] [POLXc ] by SMART
  • Other resources with information on 3C5G
  • Community annotation for 3C5G at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science