1O3Q PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES date
authors Chen, S., Vojtechovsky, J., Parkinson, G.N., Ebright, R.H., Berman, H.M.
compound source
symmetry
R_factor
R_Free 0.318
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.00
ligand CMP BindingDB enzyme
note 1O3Q supersedes 1DB7
related structures by homologous chain: 1CGP, 1O3S
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceIndirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking., Chen S, Vojtechovsky J, Parkinson GN, Ebright RH, Berman HM, J Mol Biol 2001 Nov 16;314(1):63-74. PMID:11724532
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (49 Kb) [Save to disk]
  • Biological Unit Coordinates (1o3q.pdb1.gz) 87 Kb
  • LPC: Ligand-Protein Contacts for 1O3Q
  • CSU: Contacts of Structural Units for 1O3Q
  • Likely Quarternary Molecular Structure file(s) for 1O3Q
  • Structure Factors (105 Kb)
  • Retrieve 1O3Q in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1O3Q from S2C, [Save to disk]
  • Re-refined 1o3q structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1O3Q 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 1O3Q
  • 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 1O3Q, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1o3qa1, region A:138-207 [Jmol] [rasmolscript] [script source]
        - Domain d1o3qa2, region A:8-137 [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: [1o3q_A] [1o3q_B] [1o3q_C] [1o3q]
  • SWISS-PROT database: [P0ACJ8]
  • Domain organization of [CRP_ECOLI] by SWISSPFAM
  • Domains found in 1O3Q: [HTH_CRP] [cNMP ] by SMART
    • Other resources with information on 1O3Q
  • Community annotation for 1O3Q 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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