3PZ2 | pdb_00003pz2

Crystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex with BMS3 and lipid substrate GGPP

• PDB DOI: https://doi.org/10.2210/pdb3PZ2/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-12-14 Released: 2011-05-11 
• Deposition Author(s): Guo, Z., Bon, R.S., Stigter, E.A., Waldmann, H., Alexandrov, K., Blankenfeldt, W., Goody, R.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Structure-Guided Development of Selective RabGGTase Inhibitors.

Bon, R.S., Guo, Z., Stigter, E.A., Wetzel, S., Menninger, S., Wolf, A., Choidas, A., Alexandrov, K., Blankenfeldt, W., Goody, R.S., Waldmann, H.

(2011) Angew Chem Int Ed Engl 50: 4957-4961

• PubMed: 21520375 
• DOI: https://doi.org/10.1002/anie.201101210
• Primary Citation of Related Structures:  
  3PZ1, 3PZ2, 3PZ3, 3PZ4

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Organizational Affiliation: 

Max-Planck-Institut für molekulare Physiologie, Abt. Chemische Biologie, 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: 76.34 kDa 
• Atom Count: 5,187 
• Modelled Residue Count: 620 
• Deposited Residue Count: 662 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranylgeranyl transferase type-2 subunit alpha	A	332	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	330	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3PZ	E [auth B]	(3R)-3-benzyl-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepine-7-carbonitrile C29 H29 N5 O3 S BJWZXDNEKWSGQH-RUZDIDTESA-N
GRG	F [auth B]	GERANYLGERANYL DIPHOSPHATE C20 H36 O7 P2 OINNEUNVOZHBOX-QIRCYJPOSA-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: 2.35 Å
• R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.448	α = 90
b = 84.582	β = 90
c = 117.973	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-11 
Deposition Author(s): Guo, Z., Bon, R.S., Stigter, E.A., Waldmann, H., Alexandrov, K., Blankenfeldt, W., Goody, R.S.

Revision History  

• Version 1.0: 2011-05-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-01-15
  Changes: Database references, Refinement description, Source and taxonomy
• Version 1.3: 2017-08-09
  Changes: Refinement description, Source and taxonomy
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description