6J74

Complex of GGTaseIII and full-length Ykt6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Complex of GGTaseIII and full-length Ykt6

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence 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)
Explore Q7Z6K3 
Go to UniProtKB:  Q7Z6K3
PHAROS:  Q7Z6K3
GTEx:  ENSG00000188647 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z6K3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Geranylgeranyl transferase type-2 subunit beta336Homo sapiensMutation(s): 0 
Gene Names: RABGGTBGGTB
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
GTEx:  ENSG00000137955 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53611
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence 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
GTEx:  ENSG00000106636 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15498
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.218α = 90
b = 119.218β = 90
c = 212.577γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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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: 2023-11-22
    Changes: Data collection, Database references, Refinement description