3PZ4

Crystal structure of FTase(ALPHA-subunit; BETA-subunit DELTA C10) in complex with BMS3 and lipid substrate FPP

PDB DOI: https://doi.org/10.2210/pdb3PZ4/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: 2.10 Å
R-Value Free: 0.267
R-Value Work: 0.225
R-Value Observed: 0.227

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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: 92.89 kDa
Atom Count: 6,208
Modelled Residue Count: 718
Deposited Residue Count: 805
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha	A	379	Rattus norvegicus	Mutation(s): 0 Gene Names: Fnta, Ggta, Rabggta EC: 2.5.1.58 (PDB Primary Data), 2.5.1.59 (PDB Primary Data)
UniProt
Find proteins for Q04631 (Rattus norvegicus) Explore Q04631 Go to UniProtKB: Q04631
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q04631
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein farnesyltransferase subunit beta	B	426	Rattus norvegicus	Mutation(s): 0 Gene Names: Fntb, Ggtb, Rabggtb EC: 2.5.1.58
UniProt
Find proteins for Q02293 (Rattus norvegicus) Explore Q02293 Go to UniProtKB: Q02293
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q02293
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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]
FPP Query on FPP 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]	FARNESYL DIPHOSPHATE C₁₅ H₂₈ O₇ P₂ VWFJDQUYCIWHTN-YFVJMOTDSA-N		Interactions Focus chain D [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]

Binding Affinity Annotations
ID	Source	Binding Affinity
FPP	BindingDB: 3PZ4	Kd: 2 (nM) from 1 assay(s)
3PZ	PDBBind: 3PZ4	IC50: 6 (nM) from 1 assay(s)
3PZ	BindingDB: 3PZ4	IC50: 6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.267
R-Value Work: 0.225
R-Value Observed: 0.227
Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.746	α = 90
b = 170.746	β = 90
c = 69.085	γ = 120

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: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description