1JCQ

CRYSTAL STRUCTURE OF HUMAN PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH FARNESYL DIPHOSPHATE AND THE PEPTIDOMIMETIC INHIBITOR L-739,750

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history. 



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN FARNESYLTRANSFERASE, ALPHA SUBUNIT382Homo sapiensMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49354
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN FARNESYLTRANSFERASE, BETA SUBUNIT437Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49356
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
C
2N/A
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
739
Query on 739
Download Ideal Coordinates CCD File 
G [auth B]2(S)-{2(S)-[2(R)-AMINO-3-MERCAPTO]PROPYLAMINO-3(S)-METHYL}PENTYLOXY-3-PHENYLPROPIONYLMETHIONINE SULFONE
C23 H39 N3 O6 S2
SIEXHGZWGJLLAC-OSTWSGHESA-N
FPP
Query on FPP
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F [auth B]FARNESYL DIPHOSPHATE
C15 H28 O7 P2
VWFJDQUYCIWHTN-YFVJMOTDSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
E [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACY
Query on ACY
Download Ideal Coordinates CCD File 
D [auth A]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
FPP BindingDB:  1JCQ Kd: 2 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.476α = 90
b = 178.476β = 90
c = 64.842γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-11-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    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: 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