6J7F

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

PDB DOI: https://doi.org/10.2210/pdb6J7F/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-01-18 Released: 2020-01-22
Deposition Author(s): Goto-Ito, S., Yamagata, A., Sato, Y., Fukai, S.
Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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.

Macromolecule Content

Total Structure Weight: 98.31 kDa
Atom Count: 6,533
Modelled Residue Count: 806
Deposited Residue Count: 858
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein prenyltransferase alpha subunit repeat-containing protein 1	A	327	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7Z6K3
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranylgeranyl transferase type-2 subunit beta	B	336	Homo sapiens	Mutation(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 GTEx: ENSG00000137955
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53611
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptobrevin homolog YKT6	C	195	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15498
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GER (Subject of Investigation/LOI) Query on GER Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	GERAN-8-YL GERAN C₂₀ H₃₄ HSOYJGBJQAKCNA-CAIKYXSQSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
FAR (Subject of Investigation/LOI) Query on FAR Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	FARNESYL C₁₅ H₂₆ JXBSHSBNOVLGHF-BUJBXKITSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
DPO Query on DPO Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	DIPHOSPHATE O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-J		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
TLA Query on TLA Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CMT Query on CMT	C	L-PEPTIDE LINKING	C₄ H₉ N O₂ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.88 ?
R-Value Free: 0.249
R-Value Work: 0.206
R-Value Observed: 0.208
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( ? )	Angle ( ? )
a = 119.415	α = 90
b = 119.415	β = 90
c = 210.649	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-01-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	CREST JPMJCR12M5
Japan Society for the Promotion of Science	Japan	KAKENHI 16K08574
Japan Society for the Promotion of Science	Japan	KAKENHI 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, Derived calculations, Refinement description