2R8K Replication, Transferase Dna date Sep 11, 2007
title Structure Of The Eukaryotic Dna Polymerase Eta In Complex Wi D(Gpg)-Cisplatin Containing Dna
authors T.Carell, A.Alt, K.Lammens
compound source
Molecule: Dna Polymerase Eta
Chain: A, B
Fragment: Catalytic Domain
Synonym: Radiation Sensitive Protein 30
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Yph499 (Atcc 76625)
Gene: Rad30, Dbh1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 De3 Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pexp007

Molecule: 5'-D(Dgpdtpdgpdgpdtpdgpdapdgpdc)-3'
Chain: Q, P
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Pdgpdgpdcpdtpdcpdapdcpdcpdapdc)-3'
Chain: U, T
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 41 21 2
R_factor 0.230 R_Free 0.267
length a length b length c angle alpha angle beta angle gamma
103.740 103.740 292.810 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.30 Å
ligand CA, CPT, DTP enzyme Transferase E.C. BRENDA
A, B

Primary referenceBypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta., Alt A, Lammens K, Chiocchini C, Lammens A, Pieck JC, Kuch D, Hopfner KP, Carell T, Science. 2007 Nov 9;318(5852):967-70. PMID:17991862
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (190 Kb) [Save to disk]
  • Biological Unit Coordinates (2r8k.pdb1.gz) 93 Kb
  • Biological Unit Coordinates (2r8k.pdb2.gz) 93 Kb
  • LPC: Ligand-Protein Contacts for 2R8K
  • CSU: Contacts of Structural Units for 2R8K
  • Likely Quarternary Molecular Structure file(s) for 2R8K
  • Structure Factors (170 Kb)
  • Retrieve 2R8K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2R8K from S2C, [Save to disk]
  • Re-refined 2r8k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2R8K 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 2R8K
  • 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 2R8K, from MSDmotif at EBI
  • Fold representative 2r8k from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2r8k_P] [2r8k] [2r8k_B] [2r8k_U] [2r8k_A] [2r8k_Q] [2r8k_T]
  • SWISS-PROT database: [Q04049]
  • Domain organization of [POLH_YEAST] by SWISSPFAM
  • Other resources with information on 2R8K
  • Community annotation for 2R8K 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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