3SI8 Transferase Dna date Jun 17, 2011
title Human Dna Polymerase Eta - Dna Ternary Complex With The 5'T In The Active Site (Tt2)
authors C.Biertumpfel, Y.Zhao, Y.Kondo, S.Ramon-Maiques, M.Gregory, J.Y.L C.Masutani, A.R.Lehmann, F.Hanaoka, W.Yang
compound source
Molecule: Dna Polymerase Eta
Chain: A
Fragment: Unp Residues 1-432
Synonym: Rad30 Homolog A, Xeroderma Pigmentosum Variant Typ
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: Chemically Synthesized
Gene: Polh, Rad30, Rad30a, Xpv
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3) Plyss
Expression_system_vector_type: Pet28a

Molecule: Dna (5'-D(Tpaapcp(Ttd)Paptpgpapcpgpc)
Chain: T
Engineered: Yes
Other_details: Dna Template (Chain T)

Synthetic: Yes
Other_details: Dna Oligonucleotide With Thymine Dimer (Cycl Pyrimidine Dimer, Cpd);

Molecule: Dna (5'-D(Tpgpcpgptpcpaptpa)-3')
Chain: P
Engineered: Yes
Other_details: Dna Primer (Chain P)

Synthetic: Yes
Other_details: Dna Oligonucleotide
symmetry Space Group: P 21 21 21
R_factor 0.241 R_Free 0.258
length a length b length c angle alpha angle beta angle gamma
61.236 80.259 139.759 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand 3D1, CO, DTT, DZ4, EDO, GOL, MG, TTD enzyme Transferase E.C. BRENDA
note 3SI8 supersedes 3MR4

Primary referenceStructure and mechanism of human DNA polymerase eta., Biertumpfel C, Zhao Y, Kondo Y, Ramon-Maiques S, Gregory M, Lee JY, Masutani C, Lehmann AR, Hanaoka F, Yang W, Nature. 2010 Jun 24;465(7301):1044-8. PMID:20577208
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (89 Kb) [Save to disk]
  • Biological Unit Coordinates (3si8.pdb1.gz) 83 Kb
  • LPC: Ligand-Protein Contacts for 3SI8
  • CSU: Contacts of Structural Units for 3SI8
  • Structure Factors (310 Kb)
  • Retrieve 3SI8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3SI8 from S2C, [Save to disk]
  • Re-refined 3si8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3SI8 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 3SI8
  • 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 3SI8, from MSDmotif at EBI
  • Fold representative 3si8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3si8_P] [3si8_T] [3si8] [3si8_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3SI8
  • Community annotation for 3SI8 at PDBWiki (http://pdbwiki.org)
  • 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
    Bioinformatics Unit
    Weizmann Institute of Science