4ECX Transferase Dna date Mar 26, 2012
title Human Dna Polymerase Eta - Dna Ternary Complex: Reaction In Crystal At Ph 7.0 For 300 Sec
authors T.Nakamura, Y.Zhao, W.Yang
compound source
Molecule: Dna Polymerase Eta
Chain: A
Fragment: Catalytic Core (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
Gene: Polh, Rad30, Rad30a, Xpv
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28

Molecule: Dna (5'-D(Cpaptptpaptpgpapcpgpcpt)-3'
Chain: T
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'-D(Apgpcpgptpcpaptpa)-3')
Chain: P
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 61
R_factor 0.178 R_Free 0.225
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.786 98.786 82.431 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.74 Å
ligand CA, DPO, DTP, GOL, MG enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceWatching DNA polymerase eta make a phosphodiester bond., Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W, Nature. 2012 Jul 11;487(7406):196-201. doi: 10.1038/nature11181. PMID:22785315
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (95 Kb) [Save to disk]
  • Biological Unit Coordinates (4ecx.pdb1.gz) 89 Kb
  • LPC: Ligand-Protein Contacts for 4ECX
  • CSU: Contacts of Structural Units for 4ECX
  • Structure Factors (590 Kb)
  • Retrieve 4ECX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4ECX from S2C, [Save to disk]
  • Re-refined 4ecx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4ECX 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 4ECX
  • 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 4ECX, from MSDmotif at EBI
  • Fold representative 4ecx from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ecx_P] [4ecx] [4ecx_T] [4ecx_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4ECX
  • Community annotation for 4ECX 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