6J7X

Complex of GGTaseIII, farnesyl-Ykt6, and GGPP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), and GGPP

Goto-Ito, S., Shirakawa, R., Fukai, S.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein prenyltransferase alpha subunit repeat-containing protein 1327Homo sapiensMutation(s): 0 
Gene Names: PTAR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z6K3 (Homo sapiens)
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Go to UniProtKB:  Q7Z6K3
PHAROS:  Q7Z6K3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z6K3
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Geranylgeranyl transferase type-2 subunit beta336Homo sapiensMutation(s): 0 
Gene Names: RABGGTB, GGTB
EC: 2.5.1.60
UniProt & NIH Common Fund Data Resources
Find proteins for P53611 (Homo sapiens)
Explore P53611 
Go to UniProtKB:  P53611
PHAROS:  P53611
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UniProt GroupP53611
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Synaptobrevin homolog YKT6198Homo sapiensMutation(s): 0 
Gene Names: YKT6
EC: 2.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for O15498 (Homo sapiens)
Explore O15498 
Go to UniProtKB:  O15498
PHAROS:  O15498
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15498
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GRG (Subject of Investigation/LOI)
Query on GRG
Download Ideal Coordinates CCD File 
D [auth B]GERANYLGERANYL DIPHOSPHATE
C20 H36 O7 P2
OINNEUNVOZHBOX-QIRCYJPOSA-N		 Ligand Interaction
FMT
Query on FMT
Download Ideal Coordinates CCD File 
E [auth B]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.169α = 90
b = 119.169β = 90
c = 211.006γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanCREST JPMJCR12M5
Japan Society for the Promotion of ScienceJapanKAKENHI 16K08574
Japan Society for the Promotion of ScienceJapanKAKENHI 16H05148

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Structure summary