5L1I Transferase Dna date Jul 29, 2016
title Crystal Structure Of Human Dna Polymerase Eta Inserting Dctp O6-Methyl-2'-Deoxyguanosine
authors A.Patra, 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(Cpaptp(6og)Paptpgpapcpgpcpt
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 61
R_factor 0.160 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.095 99.095 81.869 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.78 Å
ligand 6OG, CA, DCP, GOL enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMechanisms of Insertion of dCTP and dTTP Opposite the DNA lesion O6-Methyl-2'-deoxyguanosine by Human DNA Polymerase eta., Patra A, Zhang Q, Guengerich FP, Egli M, J Biol Chem. 2016 Sep 30. pii: jbc.M116.755462. PMID:27694439
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (87 Kb) [Save to disk]
  • Biological Unit Coordinates (5l1i.pdb1.gz) 82 Kb
  • LPC: Ligand-Protein Contacts for 5L1I
  • CSU: Contacts of Structural Units for 5L1I
  • Structure Factors (292 Kb)
  • Retrieve 5L1I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5L1I from S2C, [Save to disk]
  • Re-refined 5l1i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5L1I 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 5L1I
  • 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 5l1i from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5l1i_T] [5l1i_A] [5l1i_P] [5l1i]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5L1I
  • Community annotation for 5L1I at PDBWiki (http://pdbwiki.org)

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