3PZ2

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.

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

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

Organizational Affiliation

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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08602
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08603
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3PZ Query on 3PZ Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	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		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
GRG Query on GRG Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	GERANYLGERANYL DIPHOSPHATE C₂₀ H₃₆ O₇ P₂ OINNEUNVOZHBOX-QIRCYJPOSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding 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 = 66.448	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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-05-11

Deposition Author(s):

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