4G01

ARA7-GDP-Ca2+/VPS9a

Structural Biology Knowledgebase: 4G01 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.198

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4G01

Classification: TRANSPORT PROTEIN

Total Structure Weight: 50539.38

Macromolecule Entities
Molecule Chains Length Organism Details
Vacuolar protein sorting-associated protein 9A A 267 Arabidopsis thaliana Fragment: VPS9 domain, UNP residues 1-265
Gene Name(s): VPS9A VPS9 At3g19770 MMB12.26
Ras-related protein RABF2b B 181 Arabidopsis thaliana Fragment: small GTPase, UNP residues 1-179
Gene Name(s): RABF2B ARA-7 RAB5B Gene View At4g19640 F24J7.190

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

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

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.198
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 68.35 α = 90.00
b = 76.14 β = 90.00
c = 81.79 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-07-09
  • Released Date: 2013-02-27
  • Deposition author(s): Ihara, K.

Revision History

  • 2013-08-07
    Type: Citation | Details: Citation update