3MDC Lyase,Transferase Dna date Mar 30, 2010
title Dna Polymerase Lambda In Complex With Dfdctp
authors M.Garcia-Diaz, M.Murray, T.Kunkel, K.M.Chou
compound source
Molecule: Dna Polymerase Lambda
Chain: A
Synonym: Pol Lambda, Dna Polymerase Kappa, Dna Polymerase B Beta2;
Ec: 2.7.7.7, 4.2.99.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Poll
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22

Molecule: Dna (5'-D(Cpgpgpcpgpgptpapcptpg)-3')
Chain: T
Engineered: Yes

Synthetic: Yes

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

Synthetic: Yes

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

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.216 R_Free 0.266
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.206 59.773 142.008 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand GTF, MG, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe interaction between DNA polymerase lambda and anticancer nucleoside analogs., Garcia-Diaz M, Murray MS, Kunkel TA, Chou KM, J Biol Chem. 2010 Mar 26. PMID:20348107
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (71 Kb) [Save to disk]
  • Biological Unit Coordinates (3mdc.pdb1.gz) 65 Kb
  • LPC: Ligand-Protein Contacts for 3MDC
  • CSU: Contacts of Structural Units for 3MDC
  • Structure Factors (456 Kb)
  • Retrieve 3MDC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3MDC from S2C, [Save to disk]
  • Re-refined 3mdc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3MDC 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 3MDC
  • 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 3MDC, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3mdc_P] [3mdc_A] [3mdc] [3mdc_D] [3mdc_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3MDC: [HhH1] [POLXc ] by SMART
  • Other resources with information on 3MDC
  • Community annotation for 3MDC 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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