3V1D De Novo Protein, Metal Binding Protein date Dec 09, 2011
title Crystal Structure Of De Novo Designed Mid1-Cobalt
authors B.S.Der, M.Machius, M.J.Miley, B.Kuhlman
compound source
Molecule: Computational Design, Mid1-Cobalt
Chain: A, B, C, D, E, F, G, H
Synonym: Computational Redesign Of The Biological Sequence.
Engineered: Yes
 Organism_scientific: Artificial Gene
Organism_taxid: 32630
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe-80l Mbp Fusion
symmetry Space Group: P 1
R_factor 0.147 R_Free 0.194
crystal
cell
length a length b length c angle alpha angle beta angle gamma
27.720 45.451 62.112 90.04 90.00 90.00
method X-Ray Diffractionresolution 1.24 Å
ligand 1PE, CO enzyme
Primary referenceMetal-Mediated Affinity and Orientation Specificity in a Computationally Designed Protein Homodimer., Der BS, Machius M, Miley MJ, Mills JL, Szyperski T, Kuhlman B, J Am Chem Soc. 2011 Dec 15. PMID:22092237
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (217 Kb) [Save to disk]
  • Biological Unit Coordinates (3v1d.pdb1.gz) 53 Kb
  • Biological Unit Coordinates (3v1d.pdb2.gz) 53 Kb
  • Biological Unit Coordinates (3v1d.pdb3.gz) 55 Kb
  • Biological Unit Coordinates (3v1d.pdb4.gz) 55 Kb
  • LPC: Ligand-Protein Contacts for 3V1D
  • CSU: Contacts of Structural Units for 3V1D
  • Structure Factors (926 Kb)
  • Retrieve 3V1D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3V1D from S2C, [Save to disk]
  • Re-refined 3v1d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3V1D 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 3V1D
  • 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 3V1D, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3v1d_C] [3v1d_F] [3v1d_D] [3v1d_E] [3v1d_G] [3v1d_A] [3v1d_H] [3v1d_B] [3v1d]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3V1D
  • Community annotation for 3V1D at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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