3C72

Engineered RabGGTase in complex with a peptidomimetic inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3C72/pdb

• Classification: TRANSFERASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-02-06 Released: 2008-07-22 
• Deposition Author(s): Guo, Z., Wu, Y.W., Tan, K.T., Bon, R.S., Guiu-Rozas, E., Delon, C., Nguyen, U.T., Wetzel, S., Arndt, S., Goody, R.S., Blankenfeldt, W., Alexandrov, K., Waldmann, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

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

• PubMed: 18399557 
• DOI: https://doi.org/10.1002/anie.200705795
• Primary Citation of Related Structures:  
  3C72

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Organizational Affiliation: 

Max-Planck-Institut für molekulare Physiologie, Abt. Physikalische Biochemie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 76.31 kDa 
• Atom Count: 5,255 
• Modelled Residue Count: 630 
• Deposited Residue Count: 665 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranylgeranyl transferase type-2 subunit alpha	A	334	Rattus norvegicus	Mutation(s): 0  Gene Names: Rabggta, Ggta EC: 2.5.1.60
UniProt
Find proteins for Q08602 (Rattus norvegicus) Explore Q08602  Go to UniProtKB:  Q08602

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranylgeranyl transferase type-2 subunit beta	B	331	Rattus norvegicus	Mutation(s): 0  Gene Names: Rabggtb, Ggtb EC: 2.5.1.60
UniProt
Find proteins for Q08603 (Rattus norvegicus) Explore Q08603  Go to UniProtKB:  Q08603

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CX1	E [auth B]	N-[(benzyloxy)carbonyl]-L-histidyl-N-methyl-L-phenylalanyl-L-tyrosine C33 H35 N5 O7 CPZRYRVSOCXUSE-AWCRTANDSA-N
ZN	C [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.192	α = 90
b = 91.671	β = 90
c = 115.439	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-22 
Deposition Author(s): Guo, Z., Wu, Y.W., Tan, K.T., Bon, R.S., Guiu-Rozas, E., Delon, C., Nguyen, U.T., Wetzel, S., Arndt, S., Goody, R.S., Blankenfeldt, W., Alexandrov, K., Waldmann, H.

Revision History  

• Version 1.0: 2008-07-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-08-02
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description