1GK4 Vimentin date Aug 08, 2001
title Human Vimentin Coil 2b Fragment (Cys2)
authors S.V.Strelkov, H.Herrmann, N.Geisler, R.Zimbelmann, U.Aebi, P.Burkhard
compound source
Molecule: Vimentin
Chain: A, B, C, D, E, F
Fragment: Cys2, Residues 328-411
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pet-21d
symmetry Space Group: I 2 2 2
R_factor 0.242 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
76.594 84.283 240.785 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.3 Å
ligand ACT enzyme
note 1GK4 is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceConserved segments 1A and 2B of the intermediate filament dimer: their atomic structures and role in filament assembly., Strelkov SV, Herrmann H, Geisler N, Wedig T, Zimbelmann R, Aebi U, Burkhard P, EMBO J 2002 Mar 15;21(6):1255-66. PMID:11889032
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (90 Kb) [Save to disk]
  • Biological Unit Coordinates (1gk4.pdb1.gz) 30 Kb
  • Biological Unit Coordinates (1gk4.pdb2.gz) 29 Kb
  • Biological Unit Coordinates (1gk4.pdb3.gz) 29 Kb
  • LPC: Ligand-Protein Contacts for 1GK4
  • CSU: Contacts of Structural Units for 1GK4
  • Likely Quarternary Molecular Structure file(s) for 1GK4
  • Structure Factors (396 Kb)
  • Retrieve 1GK4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1GK4 from S2C, [Save to disk]
  • Re-refined 1gk4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1GK4 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 1GK4
  • 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 1GK4, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1gk4a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1gk4b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1gk4c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1gk4d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1gk4e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1gk4f_, region F [Jmol] [rasmolscript] [script source]
  • Fold representative 1gk4 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: [1gk4_F] [1gk4_E] [1gk4_A] [1gk4_C] [1gk4_D] [1gk4] [1gk4_B]
  • SWISS-PROT database: [P08670]
  • Domain organization of [VIME_HUMAN] by SWISSPFAM
  • Other resources with information on 1GK4
  • Community annotation for 1GK4 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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