1NKD Transcription Regulation date Sep 23, 1997
title Atomic Resolution (1.07 Angstroms) Structure Of The Rop Muta
authors M.Vlassi, M.Kokkinidis
compound source
Molecule: Rop
Chain: A
Synonym: Cole1 Repressor Of Primer
Engineered: Yes
Mutation: Yes
 Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.060 37.880 31.650 90.00 100.80 90.00
method X-Ray Diffractionresolution 1.09 Å
note 1NKD is a representative structure
related structures by homologous chain: 1RPO
Primary referenceStructural parameters for proteins derived from the atomic resolution (1.09 A) structure of a designed variant of the ColE1 ROP protein., Vlassi M, Dauter Z, Wilson KS, Kokkinidis M, Acta Crystallogr D Biol Crystallogr 1998 Nov 1;54(Pt 6 Pt 2):1245-60. PMID:10089502
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (26 Kb) [Save to disk]
  • Biological Unit Coordinates (1nkd.pdb1.gz) 41 Kb
  • CSU: Contacts of Structural Units for 1NKD
  • Likely Quarternary Molecular Structure file(s) for 1NKD
  • Structure Factors (403 Kb)
  • Retrieve 1NKD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NKD from S2C, [Save to disk]
  • Re-refined 1nkd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1NKD 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 1NKD
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Conformational Epitope Prediction for 1NKD from the CEP Server.
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1NKD, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nkd__, region [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: [1nkd] [1nkd_A]
  • SWISS-PROT database: [P03051]
  • Domain organization of [ROP_ECOLX] by SWISSPFAM
    • Other resources with information on 1NKD
  • Community annotation for 1NKD 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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