3PML Lyase,Transferase Dna date Nov 17, 2010
title Crystal Structure Of A Polymerase Lambda Variant With A Dgtp Opposite A Templating T
authors K.Bebenek, L.C.Pedersen, T.A.Kunkel
compound source
Molecule: Dna Polymerase Lambda
Chain: A, B
Fragment: Unp Residues 242-575
Synonym: Pol Lambda, Dna Polymerase Beta-2, Pol Beta2, Dna Kappa;
Ec:, 4.2.99.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: 562
Gene: Poll
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22

Molecule: 5'-D(Cpgpgpcptpgptpapcptpg)-3'
Chain: C, E
Engineered: Yes
Other_details: Templating Strand Dna

Synthetic: Yes

Molecule: 5'-D(Pgpcpcpg)-3'
Chain: D, G
Engineered: Yes
Other_details: Primer Strand Dna

Synthetic: Yes

Molecule: 5'-D(Cpapgptpapc)-3'
Chain: F, H
Engineered: Yes
Other_details: Downstream Strand Dna

Synthetic: Yes
symmetry Space Group: P 21 21 2
R_factor 0.233 R_Free 0.271
length a length b length c angle alpha angle beta angle gamma
97.038 191.570 59.084 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand 1GC, MG, NA enzyme Transferase E.C. BRENDA
A, B

Primary referenceReplication infidelity via a mismatch with Watson-Crick geometry., Bebenek K, Pedersen LC, Kunkel TA, Proc Natl Acad Sci U S A. 2011 Jan 13. PMID:21233421
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (134 Kb) [Save to disk]
  • Biological Unit Coordinates (3pml.pdb1.gz) 64 Kb
  • Biological Unit Coordinates (3pml.pdb2.gz) 67 Kb
  • LPC: Ligand-Protein Contacts for 3PML
  • CSU: Contacts of Structural Units for 3PML
  • Structure Factors (386 Kb)
  • Retrieve 3PML in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PML from S2C, [Save to disk]
  • Re-refined 3pml structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PML 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 3PML
  • 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 3PML, from MSDmotif at EBI
  • Fold representative 3pml from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pml_D] [3pml_A] [3pml_H] [3pml] [3pml_B] [3pml_E] [3pml_C] [3pml_F] [3pml_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3PML: [HhH1] [POLXc ] by SMART
  • Other resources with information on 3PML
  • Community annotation for 3PML 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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