1VG0

The crystal structures of the REP-1 protein in complex with monoprenylated Rab7 protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.188

Literature

Macromolecules
Sequence Display for 1VG0

Classification: PROTEIN BINDING / PROTEIN TRANSPORT

Total Structure Weight: 97124.65

Macromolecule Entities
Molecule Chains Length Organism Details
Rab proteins geranylgeranyltransferase component A 1 A 650 Rattus norvegicus Mutation: Q231K, K462R, A473T, G483A
Gene Name(s): Chm Rep1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ras-related protein Rab-7 B 207 Rattus norvegicus Gene Name(s): Rab7a Rab7
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 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)
GER
Query on GER

A GERAN-8-YL GERAN
C20 H34
HSOYJGBJQAKCNA-CAIKYXSQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PG4
Query on PG4

B TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
GER N/A in BindingDB
Kd: 0.8 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.188
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 64.30 α = 90.00
b = 105.30 β = 90.00
c = 132.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-04-22
  • Released Date: 2004-07-20
  • Deposition author(s): Rak, A., Pylypenko, O., Niculae, A., Pyatkov, K., Goody, R.S., Alexandrov, K.

Revision History

  • Version 1_0: 2004-07-20

    Type: Initial release

  • Version 1_1: 2008-04-27

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance

  • Version 1_3: 2017-10-04

    Type: Refinement description