6J7F

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.0 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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein prenyltransferase alpha subunit repeat-containing protein 1 A327Homo sapiensMutation(s): 0 
Gene Names: PTAR1
Find proteins for Q7Z6K3 (Homo sapiens)
Explore Q7Z6K3 
Go to UniProtKB:  Q7Z6K3
NIH Common Fund Data Resources
PHAROS:  Q7Z6K3
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Geranylgeranyl transferase type-2 subunit beta B336Homo sapiensMutation(s): 0 
Gene Names: RABGGTBGGTB
EC: 2.5.1.60
Find proteins for P53611 (Homo sapiens)
Explore P53611 
Go to UniProtKB:  P53611
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PHAROS:  P53611
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Synaptobrevin homolog YKT6 C195Homo sapiensMutation(s): 0 
Gene Names: YKT6
EC: 2.3.1
Find proteins for O15498 (Homo sapiens)
Explore O15498 
Go to UniProtKB:  O15498
NIH Common Fund Data Resources
PHAROS:  O15498
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GER
Query on GER

Download Ideal Coordinates CCD File 
B
GERAN-8-YL GERAN
C20 H34
HSOYJGBJQAKCNA-CAIKYXSQSA-N
 Ligand Interaction
FAR
Query on FAR

Download Ideal Coordinates CCD File 
B
FARNESYL
C15 H26
JXBSHSBNOVLGHF-BUJBXKITSA-N
 Ligand Interaction
DPO
Query on DPO

Download Ideal Coordinates CCD File 
B
DIPHOSPHATE
O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-J
 Ligand Interaction
TLA
Query on TLA

Download Ideal Coordinates CCD File 
B
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CMT
Query on CMT
CL-PEPTIDE LINKINGC4 H9 N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.415α = 90
b = 119.415β = 90
c = 210.649γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



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