1K5D

Crystal structure of Ran-GPPNHP-RanBP1-RanGAP complex

Structural Biology Knowledgebase: 1K5D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.267
  • R-Value Work: 0.237

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1K5D

Classification: SIGNALING PROTEIN / SIGNALING ACTIVATOR

Total Structure Weight: 366513.16

Macromolecule Entities
Molecule Chains Length Organism Details
GTP-binding nuclear protein RAN A, D, G, J 216 Homo sapiens Gene Name(s): RAN Gene View ARA24 OK/SW-cl.81
Ran-specific GTPase-activating protein B, E, H, K 201 Homo sapiens Gene Name(s): RANBP1 Gene View
Ran GTPase activating protein 1 C, F, I, L 386 Schizosaccharomyces pombe Mutation: S2A
Gene Name(s): rna1 SPAC22E12.07

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GNP
Query on GNP

A, D, G, J PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, D, G, J MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.267
  • R-Value Work: 0.237
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 101.55 α = 71.59
b = 103.11 β = 80.55
c = 120.18 γ = 67.78

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-10-10
  • Released Date: 2002-02-13
  • Deposition author(s): Seewald, M.J., Koerner, C., Wittinghofer, A., Vetter, I.R.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4