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
Ec: 2.7.7.7
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
crystal
cell
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.2.7.7.7 BRENDA
note 3SI8 supersedes 3MR4
Gene
Ontology
ChainFunctionProcessComponent
A


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.

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