2D4H Signaling Protein date Oct 19, 2005
title Crystal-Structure Of The N-Terminal Large Gtpase Domain Of H Guanylate Binding Protein 1 (Hgbp1) In Complex With Gmp
authors A.Ghosh, G.J.K.Praefcke, L.Renault, A.Wittinghofer, C.Herrmann
compound source
Molecule: Interferon-Induced Guanylate-Binding Protein 1
Chain: A, B
Fragment: N-Terminal Large Gtpase Domain
Synonym: Gtp-Binding Protein 1, Guanine Nucleotide-Binding Hugbp-1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gbp1
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe9
symmetry Space Group: P 1 21 1
R_factor 0.233 R_Free 0.275
length a length b length c angle alpha angle beta angle gamma
39.921 173.450 49.632 90.00 110.85 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand 5GP enzyme
A, B

Primary referenceHow guanylate-binding proteins achieve assembly-stimulated processive cleavage of GTP to GMP., Ghosh A, Praefcke GJ, Renault L, Wittinghofer A, Herrmann C, Nature. 2006 Mar 2;440(7080):101-4. PMID:16511497
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (103 Kb) [Save to disk]
  • Biological Unit Coordinates (2d4h.pdb1.gz) 51 Kb
  • Biological Unit Coordinates (2d4h.pdb2.gz) 48 Kb
  • LPC: Ligand-Protein Contacts for 2D4H
  • CSU: Contacts of Structural Units for 2D4H
  • Likely Quarternary Molecular Structure file(s) for 2D4H
  • Structure Factors (107 Kb)
  • Retrieve 2D4H in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2D4H from S2C, [Save to disk]
  • Re-refined 2d4h structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2D4H 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 2D4H
  • 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 2D4H, from MSDmotif at EBI
  • Fold representative 2d4h from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2d4h_A] [2d4h] [2d4h_B]
  • SWISS-PROT database: [P32455]
  • Domain organization of [GBP1_HUMAN] by SWISSPFAM
  • Other resources with information on 2D4H
  • Community annotation for 2D4H 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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