2G77

Crystal Structure of Gyp1 TBC domain in complex with Rab33 GTPase bound to GDP and AlF3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.205

Literature

Macromolecules
Sequence Display for 2G77

Classification: HYDROLASE ACTIVATOR / PROTEIN TRANSPORT

Total Structure Weight: 71259.11

Macromolecule Entities
Molecule Chains Length Organism Details
GTPase-activating protein GYP1 A 410 Saccharomyces cerevisiae Fragment: Gyp1 TBC domain
Mutation: E405K
Gene Name(s): GYP1 YOR070C YOR29-21
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ras-related protein Rab-33B B 198 Mus musculus Mutation: M116M, M119M, M172M, M193M
Gene Name(s): Rab33b
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
AF3
Query on AF3

B ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.244
  • R-Value Work: 0.205
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 72.20 α = 90.00
b = 94.53 β = 90.00
c = 102.56 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-02-27
  • Released Date: 2006-07-25
  • Deposition author(s): Pan, X., Eathiraj, S., Munson, M., Lambright, D.G.

Revision History

  • 2008-05-01
    Type: Version format compliance
  • 2011-07-13
    Type: Version format compliance