3C72

Engineered RabGGTase in complex with a peptidomimetic inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Development of selective RabGGTase inhibitors and crystal structure of a RabGGTase-inhibitor complex.

Guo, Z.Wu, Y.W.Tan, K.T.Bon, R.S.Guiu-Rozas, E.Delon, C.Nguyen, T.U.Wetzel, S.Arndt, S.Goody, R.S.Blankenfeldt, W.Alexandrov, K.Waldmann, H.

(2008) Angew.Chem.Int.Ed.Engl. 47: 3747-3750


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Geranylgeranyl transferase type-2 subunit alpha
A
334Rattus norvegicusMutation(s): 0 
Gene Names: Rabggta (Ggta)
EC: 2.5.1.60
Find proteins for Q08602 (Rattus norvegicus)
Go to UniProtKB:  Q08602
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Geranylgeranyl transferase type-2 subunit beta
B
331Rattus norvegicusMutation(s): 0 
Gene Names: Rabggtb (Ggtb)
EC: 2.5.1.60
Find proteins for Q08603 (Rattus norvegicus)
Go to UniProtKB:  Q08603
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CX1
Query on CX1

Download SDF File 
Download CCD File 
B
N-[(benzyloxy)carbonyl]-L-histidyl-N-methyl-L-phenylalanyl-L-tyrosine
C33 H35 N5 O7
CPZRYRVSOCXUSE-AWCRTANDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CX1IC50: 22700 nM BINDINGMOAD
CX1IC50: 22700 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.192α = 90.00
b = 91.671β = 90.00
c = 115.439γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-08-02
    Type: Refinement description, Source and taxonomy