9HJZ | pdb_00009hjz

Crystal structure of human geranylgeranyl diphosphate synthase mutant Y246D

• PDB DOI: https://doi.org/10.2210/pdb9HJZ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-12-02 Released: 2025-06-25 
• Deposition Author(s): Yehia, R., Giladi, M., Haitin, Y.
• Funding Organization(s): Israel Science Foundation, Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 
  0.253 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human geranylgeranyl diphosphate synthase mutant Y246D

Yehia, R., Portasikova, J.M., Kadek, A., Man, P., Giladi, M., Haitin, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 70.97 kDa 
• Atom Count: 4,396 
• Modeled Residue Count: 565 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranylgeranyl pyrophosphate synthase	A, B	307	Homo sapiens	Mutation(s): 2  Gene Names: GGPS1 EC: 2.5.1 (PDB Primary Data), 2.5.1.1 (PDB Primary Data), 2.5.1.29 (PDB Primary Data), 2.5.1.10 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O95749 (Homo sapiens) Explore O95749  Go to UniProtKB:  O95749
PHAROS:  O95749 GTEx:  ENSG00000152904

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free:  0.253 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 192.731	α = 90
b = 192.731	β = 90
c = 97.635	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-25 
Deposition Author(s): Yehia, R., Giladi, M., Haitin, Y.

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Funding Organization	Location	Grant Number
Israel Science Foundation	Israel	1721/16
Israel Science Foundation	Israel	1653/21
Other private	Israel	ICRF 01214
Other private	Israel	ICRF 19202
Other private	Israel	Israel Cancer Association 20230029
Other private	Israel	Kahn Foundation's Orion project
Other private	Israel	Karl and Leonora Fingerhut Fund for Cancer Research
Other private	Israel	Recanati Foundation

Revision History  

• Version 1.0: 2025-06-25
  Type: Initial release