3E37

Protein farnesyltransferase complexed with bisubstrate ethylenediamine scaffold inhibitor 5

• PDB DOI: https://doi.org/10.2210/pdb3E37/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-06 Released: 2009-03-10 
• Deposition Author(s): Hast, M.A., Beese, L.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.190 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 94.3 kDa 
• Atom Count: 6,707 
• Modelled Residue Count: 725 
• Deposited Residue Count: 816 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha	A	379	Homo sapiens	Mutation(s): 0  Gene Names: FNTA EC: 2.5.1.58 (PDB Primary Data), 2.5.1.59 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P49354 (Homo sapiens) Explore P49354  Go to UniProtKB:  P49354
PHAROS:  P49354 GTEx:  ENSG00000168522

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein farnesyltransferase subunit beta	B	437	Homo sapiens	Mutation(s): 0  Gene Names: FNTB EC: 2.5.1.58
UniProt & NIH Common Fund Data Resources
Find proteins for P49356 (Homo sapiens) Explore P49356  Go to UniProtKB:  P49356
PHAROS:  P49356 GTEx:  ENSG00000257365

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan:  G05551OP GlyCosmos:  G05551OP

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ED5	D [auth B]	tert-butyl 4-({(2-{(4-cyanophenyl)[(1-methyl-1H-imidazol-5-yl)methyl]amino}ethyl)[(2-methylphenyl)sulfonyl]amino}methyl)piperidine-1-carboxylate C32 H42 N6 O4 S CHEKEDNUVFBGCF-UHFFFAOYSA-N
ZN	E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ED5	BindingDB:  3E37	IC50: 4050 (nM) from 1 assay(s)
	Binding MOAD:  3E37	IC50: 4050 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	C	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.190 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 178.386	α = 90
b = 178.386	β = 90
c = 64.51	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-10 
Deposition Author(s): Hast, M.A., Beese, L.S.

Revision History  

• Version 1.0: 2009-03-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-02-21
  Changes: Data collection, Database references, Structure summary