3PZ2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Geranylgeranyl transferase type-2 subunit alpha332Rattus norvegicusMutation(s): 0 
Gene Names: RabggtaGgta
EC: 2.5.1.60
UniProt
Find proteins for Q08602 (Rattus norvegicus)
Explore Q08602 
Go to UniProtKB:  Q08602
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08602
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Geranylgeranyl transferase type-2 subunit beta330Rattus norvegicusMutation(s): 0 
Gene Names: RabggtbGgtb
EC: 2.5.1.60
UniProt
Find proteins for Q08603 (Rattus norvegicus)
Explore Q08603 
Go to UniProtKB:  Q08603
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08603
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3PZ
Query on 3PZ

Download Ideal Coordinates CCD File 
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
Query on GRG

Download Ideal Coordinates CCD File 
F [auth B]GERANYLGERANYL DIPHOSPHATE
C20 H36 O7 P2
OINNEUNVOZHBOX-QIRCYJPOSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
3PZ PDBBind:  3PZ2 IC50: 724 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.448α = 90
b = 84.582β = 90
c = 117.973γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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