5DLG Transferase Dna date Sep 04, 2015
title Crystal Structure Of Human Dna Polymerase Eta Inserting Dgmp Opposite O4-Methylhymidine
authors A.Patra, D.K.Oflaherty, M.Egli
compound source
Molecule: Dna Polymerase Eta
Chain: A
Synonym: Rad30 Homolog A,Xeroderma Pigmentosum Variant Type
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

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Chemically Synthesized

Molecule: Dna (5'-D(Cpaptp(5db)Paptpgpapcpgpcpt
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Chemically Synthesized
symmetry Space Group: P 61
R_factor 0.172 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.656 98.656 82.131 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.35 Å
ligand 5DB, GOL, MG, XG4 enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceLesion Orientation of O(4)-Alkylthymidine Influences Replication by Human DNA Polymerase eta., O'Flaherty DK, Patra A, Su Y, Guengerich FP, Egli M, Wilds CJ, Chem Sci. 2016 Aug 1;7(8):4896-4904. doi: 10.1039/C6SC00666C. Epub 2016 Apr 26. PMID:27574558
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (88 Kb) [Save to disk]
  • Biological Unit Coordinates (5dlg.pdb1.gz) 83 Kb
  • LPC: Ligand-Protein Contacts for 5DLG
  • CSU: Contacts of Structural Units for 5DLG
  • Structure Factors (519 Kb)
  • Retrieve 5DLG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DLG from S2C, [Save to disk]
  • Re-refined 5dlg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5DLG 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 5DLG
  • 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
  • Fold representative 5dlg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dlg] [5dlg_T] [5dlg_A] [5dlg_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5DLG
  • Community annotation for 5DLG at PDBWiki (http://pdbwiki.org)

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