1RUN Transcription Dna date May 26, 1996
title Catabolite Gene Activator Protein (Cap)Dna Complex + Adenosine-3',5'-Cyclic-Monophosphate
authors G.N.Parkinson, A.Gunasekera, J.Vojtechovsky, X.Zhang, T.A.Kunkel, H.M.Berman, R.H.Ebright
compound source
Molecule: Dna (5'- D(Gpcpgpapapapapaptpgptpgpapt)-3');
Chain: C, E
Engineered: Yes
Synthetic: Yes

Molecule: Dna (5'- D(Cptpapgpaptpcpapcpaptptptptptpcpg )-3');
Chain: D, F
Engineered: Yes

Synthetic: Yes

Molecule: Protein (Catabolite Gene Activator Protein (Cap) );
Chain: A, B
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 2 2 21
R_factor 0.207 R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
136.930 152.800 76.000 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand CMP BindingDB enzyme
related structures by homologous chain: 1J59, 1RUO
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceAromatic hydrogen bond in sequence-specific protein DNA recognition., Parkinson G, Gunasekera A, Vojtechovsky J, Zhang X, Kunkel TA, Berman H, Ebright RH, Nat Struct Biol 1996 Oct;3(10):837-41. PMID:8836098
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (101 Kb) [Save to disk]
  • Biological Unit Coordinates (1run.pdb1.gz) 95 Kb
  • LPC: Ligand-Protein Contacts for 1RUN
  • CSU: Contacts of Structural Units for 1RUN
  • Likely Quarternary Molecular Structure file(s) for 1RUN
  • Structure Factors (142 Kb)
  • Retrieve 1RUN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RUN from S2C, [Save to disk]
  • Re-refined 1run structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1RUN 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 1RUN
  • 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
  • 3D motif for 1RUN, from MSDmotif at EBI
  • Genome occurence of 1RUN's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1runa1, region A:138-209 [Jmol] [rasmolscript] [script source]
        - Domain d1runa2, region A:9-137 [Jmol] [rasmolscript] [script source]
        - Domain d1runb1, region B:138-205 [Jmol] [rasmolscript] [script source]
        - Domain d1runb2, region B:9-137 [Jmol] [rasmolscript] [script source]
  • Fold representative 1run from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1run_A] [1run_C] [1run_E] [1run] [1run_B] [1run_D] [1run_F]
  • SWISS-PROT database: [P0ACJ8]
  • Domain organization of [CRP_ECOLI] by SWISSPFAM
  • Domains found in 1RUN: [HTH_CRP] [cNMP ] by SMART
  • Other resources with information on 1RUN
  • Community annotation for 1RUN 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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