2EFC

Ara7-GDP/AtVps9a

Structural Biology Knowledgebase: 2EFC SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.221

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2EFC

Classification: TRANSPORT PROTEIN

Total Structure Weight: 100998.61

Macromolecule Entities
Molecule Chains Length Organism Details
Similarity to vacuolar protein sorting-associated protein VPS9 A, C 267 Arabidopsis thaliana Fragment: Vps9 domain
Gene Name(s): VPS9A VPS9 At3g19770 MMB12.26
Small GTP-binding protein-like B, D 181 Arabidopsis thaliana Fragment: GTPase domain
Gene Name(s): RABF2B ARA-7 RAB5B Gene View At4g19640 F24J7.190

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GDP
Query on GDP

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.221
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 58.38 α = 81.68
b = 58.47 β = 86.89
c = 68.71 γ = 72.97

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-02-22
  • Released Date: 2008-02-26
  • Deposition author(s): Uejima, T., Ihara, K., Goh, T., Ito, E., Sunada, M., Ueda, T., Nakano, A., Wakatsuki, S.

Revision History

  • 2011-12-21
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values