1DGS Ligase date Nov 25, 1999
title Crystal Structure Of Nad+-Dependent Dna Ligase From T. Filiformis
authors J.Y.Lee, C.Chang, H.K.Song, S.T.Kwon, S.W.Suh
compound source
Molecule: Dna Ligase
Chain: A, B
Ec: 6.5.1.2
Other_details: Amp Is Bonded To Lys116
 Organism_scientific: Thermus Filiformis
Organism_taxid: 276
symmetry Space Group: P 1 21 1
R_factor 0.228 R_Free 0.298
crystal
cell
length a length b length c angle alpha angle beta angle gamma
89.210 117.330 97.480 90.00 115.09 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand AMP, ZN enzyme Ligase E.C.6.5.1.2 BRENDA
note 1DGS (Molecule of the Month:pdb55)
related structures by homologous chain: 1V9P
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications., Lee JY, Chang C, Song HK, Moon J, Yang JK, Kim HK, Kwon ST, Suh SW, EMBO J 2000 Mar 1;19(5):1119-29. PMID:10698952
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (203 Kb) [Save to disk]
  • Biological Unit Coordinates (1dgs.pdb1.gz) 100 Kb
  • Biological Unit Coordinates (1dgs.pdb2.gz) 100 Kb
  • LPC: Ligand-Protein Contacts for 1DGS
  • CSU: Contacts of Structural Units for 1DGS
  • Likely Quarternary Molecular Structure file(s) for 1DGS
  • Structure Factors (291 Kb)
  • Retrieve 1DGS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DGS from S2C, [Save to disk]
  • Re-refined 1dgs structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1DGS 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 1DGS
  • 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
  • 3D motif for 1DGS, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dgsa3, region A:1-314 [Jmol] [rasmolscript] [script source]
        - Domain d1dgsa2, region A:315-400 [Jmol] [rasmolscript] [script source]
        - Domain d1dgsa1, region A:401-581 [Jmol] [rasmolscript] [script source]
        - Domain d1dgsb3, region B:2001-2314 [Jmol] [rasmolscript] [script source]
        - Domain d1dgsb2, region B:2315-2400 [Jmol] [rasmolscript] [script source]
        - Domain d1dgsb1, region B:2401-2581 [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1dgs_B] [1dgs] [1dgs_A]
  • SWISS-PROT database: [Q9ZHI0]
  • Domain organization of [DNLJ_THEFI] by SWISSPFAM
  • Domains found in 1DGS: [BRCT] [HhH1] [LIGANc ] by SMART
    • Other resources with information on 1DGS
  • Community annotation for 1DGS at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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