3MR5 Transferase Dna date Apr 28, 2010
title Human Dna Polymerase Eta - Dna Ternary Complex With A Cpd 1b Of The Active Site (Tt3)
authors C.Biertumpfel, Y.Zhao, S.Ramon-Maiques, M.T.Gregory, J.Y.Lee, W.Y
compound source
Molecule: Dna Polymerase Eta
Chain: A
Fragment: Catalytic Core (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
Gene: Polh, Rad30, Rad30a, Xpv
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector: Plasmid
Expression_system_plasmid: Pet28

Molecule: Dna (5'-D(Tpapapcp(Ttd)Paptpgpapcpgpa
Chain: T
Fragment: Dna Template
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'-D(Apcpgptpcpaptpapa)-3')
Chain: P
Fragment: Dna Primer
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 61
R_factor 0.191 R_Free 0.207
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.125 99.125 81.703 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.80 Å
ligand GOL, MG, TTD, XG4 enzyme Transferase E.C.2.7.7.7 BRENDA
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] (95 Kb) [Save to disk]
  • Biological Unit Coordinates (3mr5.pdb1.gz) 89 Kb
  • LPC: Ligand-Protein Contacts for 3MR5
  • CSU: Contacts of Structural Units for 3MR5
  • Structure Factors (478 Kb)
  • Retrieve 3MR5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3MR5 from S2C, [Save to disk]
  • Re-refined 3mr5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3MR5 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 3MR5
  • 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 3MR5, from MSDmotif at EBI
  • Fold representative 3mr5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3mr5] [3mr5_T] [3mr5_P] [3mr5_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3MR5
  • Community annotation for 3MR5 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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