1I4D

CRYSTAL STRUCTURE ANALYSIS OF RAC1-GDP COMPLEXED WITH ARFAPTIN (P21)

Structural Biology Knowledgebase: 1I4D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.298
  • R-Value Work: 0.238

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1I4D

Classification: Signaling Protein

Total Structure Weight: 73174.33

Macromolecule Entities
Molecule Chains Length Organism Details
ARFAPTIN 2 A, B 224 Homo sapiens Fragment: RESIDUES 118-341
Gene Name(s): ARFIP2 Gene View POR1
RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 D 192 Homo sapiens Gene Name(s): RAC1 Gene View TC25 MIG5

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

D GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
GDP N/A in BindingDB
Kd: 3000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.298
  • R-Value Work: 0.238
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 63.57 α = 90.00
b = 47.46 β = 97.51
c = 125.31 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-02-20
  • Released Date: 2001-05-16
  • Deposition author(s): Tarricone, C., Xiao, B., Justin, N., Gamblin, S.J., Smerdon, S.J.

Revision History

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