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
  • Alignments of the sequence of 3MR5 with the sequences similar proteins can be viewed for 3MR5's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • 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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