6P0D Ligase date May 16, 2019
title Human Dna Ligase 1 (E346ae592a) Bound To An Adenylated, Hyd Terminated Dna Nick
authors M.J.Schellenberg, R.S.Williams, P.S.Tumbale, A.A.Riccio
compound source
Molecule: Dna Ligase 1
Chain: A
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 Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmcsg7

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgptpc)-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(Gptpcpcpgpapcpgpapcpgpcpaptpcpapgpc)-3'
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.160 R_Free 0.179
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.793 101.227 115.368 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.75 Å
ligand AMP, PEG enzyme Ligase E.C.6.5.1.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (383 Kb) [Save to disk]
  • Biological Unit Coordinates (6p0d.pdb1.gz) 376 Kb
  • LPC: Ligand-Protein Contacts for 6P0D
  • CSU: Contacts of Structural Units for 6P0D
  • Structure Factors (2507 Kb)
  • Retrieve 6P0D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6P0D from S2C, [Save to disk]
  • View 6P0D 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 6P0D
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6p0d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6p0d_C] [6p0d_A] [6p0d_D] [6p0d_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6P0D
  • Community annotation for 6P0D at PDBWiki (http://pdbwiki.org)

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