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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Geranylgeranyl transferase type-2 subunit alpha
A
332Rattus 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
330Rattus 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 4 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
3PZ
Query on 3PZ

Download SDF File 
Download CCD File 
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
 Ligand Interaction
GRG
Query on GRG

Download SDF File 
Download CCD File 
B
GERANYLGERANYL DIPHOSPHATE
C20 H36 O7 P2
OINNEUNVOZHBOX-QIRCYJPOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3PZIC50: 724 nM BINDINGMOAD
3PZIC50: 724 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.448α = 90.00
b = 84.582β = 90.00
c = 117.973γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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