1F5N

HUMAN GUANYLATE BINDING PROTEIN-1 IN COMPLEX WITH THE GTP ANALOGUE, GMPPNP.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Triphosphate structure of guanylate-binding protein 1 and implications for nucleotide binding and GTPase mechanism.

Prakash, B.Renault, L.Praefcke, G.J.Herrmann, C.Wittinghofer, A.

(2000) EMBO J. 19: 4555-4564

  • DOI: 10.1093/emboj/19.17.4555
  • Also Cited By: 2D4H, 2BC9, 2B92, 2B8W

  • PubMed Abstract: 
  • The interferon-gamma-induced guanylate-binding protein 1 (GBP1) belongs to a special class of large GTP- binding proteins of 60-100 kDa with unique characteristics. Here we present the structure of human GBP1 in complex with the non-hydrolysable GTP ...

    The interferon-gamma-induced guanylate-binding protein 1 (GBP1) belongs to a special class of large GTP- binding proteins of 60-100 kDa with unique characteristics. Here we present the structure of human GBP1 in complex with the non-hydrolysable GTP analogue GppNHp. Basic features of guanine nucleotide binding, such as the P-loop orientation and the Mg(2+) co-ordination, are analogous to those of Ras-related and heterotrimeric GTP-binding proteins. However, the glycosidic bond and thus the orientation of the guanine base and its interaction with the protein are very different. Furthermore, two unique regions around the base and the phosphate-binding areas, the guanine and the phosphate caps, respectively, give the nucleotide-binding site a unique appearance not found in the canonical GTP-binding proteins. The phosphate cap, which constitutes the region analogous to switch I, completely shields the phosphate-binding site from solvent such that a potential GTPase-activating protein cannot approach. This has consequences for the GTPase mechanism of hGBP1 and possibly of other large GTP-binding proteins.


    Related Citations: 
    • Structure of human Guanylate Binding Protein-1 representing a unique class of GTP binding proteins
      Prakash, B.,Praefcke, G.J.K.,Renault, L.,Wittinghofer, A.,Herrmann, C.
      (2000) Nature 403: 567
    • Nucleotide-binding Characteristics of Human Guanylate-binding protein 1(hGBP1) and Identification of the Third GTP-binding Motif
      Praefcke, G.J.K.,Geyer, M.,Schwemmle, M.,Kalbitzer, H.R.,Herrmann, C.
      (1999) J.Mol.Biol. 292: 321


    Organizational Affiliation

    Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Strabetae 11, D-44227 Dortmund, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INTERFERON-INDUCED GUANYLATE-BINDING PROTEIN 1
A
592Homo sapiensMutation(s): 0 
Gene Names: GBP1
EC: 3.6.5.-
Find proteins for P32455 (Homo sapiens)
Go to Gene View: GBP1
Go to UniProtKB:  P32455
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

Download SDF File 
Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.226 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 161.228α = 90.00
b = 42.652β = 100.19
c = 91.544γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
CNSrefinement
AMoREphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description
  • Version 1.4: 2018-01-31
    Type: Experimental preparation