1LD7

Co-crystal structure of Human Farnesyltransferase with farnesyldiphosphate and inhibitor compound 66

• PDB DOI: https://doi.org/10.2210/pdb1LD7/pdb

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


• Deposited: 2002-04-08 Released: 2002-06-19 
• Deposition Author(s): Taylor, J.S., Terry, K.L., Beese, L.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.219 
• R-Value Work: 0.195 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 94.93 kDa 
• Atom Count: 6,479 
• Modelled Residue Count: 720 
• Deposited Residue Count: 819 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protein farnesyltransferase alpha subunit	A	382	Homo sapiens	Mutation(s): 0  EC: 2.5.1
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 beta subunit	B	437	Homo sapiens	Mutation(s): 0  EC: 2.5.1
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U66	F [auth B]	(20S)-19,20,22,23-TETRAHYDRO-19-OXO-5H,21H-18,20-ETHANO-12,14-ETHENO-6,10-METHENOBENZ[D]IMIDAZO[4,3-L][1,6,9,13]OXATRIA ZACYCLONOADECOSINE-9-CARBONITRILE C27 H27 N5 O2 GBEQWWUQNVMGMR-LLHWJCAFSA-N
FPP	E [auth B]	FARNESYL DIPHOSPHATE C15 H28 O7 P2 VWFJDQUYCIWHTN-YFVJMOTDSA-N
ZN	D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FPP	BindingDB:  1LD7	Kd: 2 (nM) from 1 assay(s)
U66	Binding MOAD:  1LD7	IC50: 1.1 (nM) from 1 assay(s)
	PDBBind:  1LD7	IC50: 1.1 (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: 2.00 Å
• R-Value Free: 0.219 
• R-Value Work: 0.195 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 178.725	α = 90
b = 178.725	β = 90
c = 64.549	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-06-19 
Deposition Author(s): Taylor, J.S., Terry, K.L., Beese, L.S.

Revision History  

• Version 1.0: 2002-06-19
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-08-16
  Changes: Data collection, Database references, Refinement description, Structure summary