2GF9

Crystal structure of human RAB3D in complex with GDP

Structural Biology Knowledgebase: 2GF9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.185
  • R-Value Work: 0.153

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2GF9

Classification: PROTEIN TRANSPORT

Total Structure Weight: 22141.11

Macromolecule Entities
Molecule Chains Length Organism Details
Ras-related protein Rab-3D A 189 Homo sapiens Fragment: residues 20-189
Gene Name(s): RAB3D Gene View GOV RAB16

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

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

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UNX
Query on UNX

A UNKNOWN ATOM OR ION
X
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.185
  • R-Value Work: 0.153
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 35.70 α = 90.00
b = 63.22 β = 90.00
c = 67.69 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-03-21
  • Released Date: 2006-05-02
  • Deposition author(s): Hong, B., Wang, J., Shen, L., Tempel, W., Landry, R., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History

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