6P0E Ligase date May 16, 2019
title Human Dna Ligase 1 (E346a,E592a) Bound To Adenylated Dna Con 8-Oxo Guanine:Adenine Base-Pair
authors M.J.Schellenberg, R.S.Williams, P.S.Tumbale, A.A.Riccio
compound source
Molecule: Dna Ligase 1
Chain: A
Fragment: Residues 262-904
Synonym: Dna Ligase I,Polydeoxyribonucleotide Synthase [Atp
Ec: 6.5.1.1
Engineered: Yes
Mutation: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lig1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgptp(8og))-3
Chain: B
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Pgptpcpgpgpapc)-3')
Chain: C
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Gptpcpcpgpapcpapapcpgpcpaptpcpapgpc)-3'
Chain: D
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.155 R_Free 0.184
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.676 100.939 115.360 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand 8OG, AMP, PEG, TRS enzyme Ligase E.C.6.5.1.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (369 Kb) [Save to disk]
  • Biological Unit Coordinates (6p0e.pdb1.gz) 361 Kb
  • LPC: Ligand-Protein Contacts for 6P0E
  • CSU: Contacts of Structural Units for 6P0E
  • Structure Factors (2214 Kb)
  • Retrieve 6P0E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6P0E from S2C, [Save to disk]
    • View 6P0E 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 6P0E
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6p0e_A] [6p0e_C] [6p0e_B] [6p0e_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6P0E
  • Community annotation for 6P0E at PDBWiki (http://pdbwiki.org)

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