9HJS | pdb_00009hjs

Crystal structure of human geranylgeranyl diphosphate synthase mutant R235C

PDB DOI: https://doi.org/10.2210/pdb9HJS/pdb

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

Deposited: 2024-12-01 Released: 2025-06-25
Deposition Author(s): Yehia, R., Giladi, M., Haitin, Y.
Funding Organization(s): Israel Science Foundation, Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free:
0.271 (Depositor), 0.271 (DCC)
R-Value Work:
0.227 (Depositor), 0.227 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of human geranylgeranyl diphosphate synthase mutant R235C

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

To be published.

Macromolecule Content

Total Structure Weight: 215.29 kDa
Atom Count: 13,669
Modeled Residue Count: 1,752
Deposited Residue Count: 1,842
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranylgeranyl pyrophosphate synthase	A, B, C, D, E A, B, C, D, E, F	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O95749
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GRG (Subject of Investigation/LOI) Query on GRG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain S [auth E] SDF format, chain V [auth F] SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain S [auth E] MOL2 format, chain V [auth F] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain S [auth E] mmCIF format, chain V [auth F] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B]	G [auth A] J [auth B] M [auth C] P [auth D] S [auth E] G [auth A], J [auth B], M [auth C], P [auth D], S [auth E], V [auth F]	GERANYLGERANYL DIPHOSPHATE C₂₀ H₃₆ O₇ P₂ OINNEUNVOZHBOX-QIRCYJPOSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain X [auth F] SDF format, chain W [auth F] SDF format, chain U [auth E] SDF format, chain T [auth E] SDF format, chain R [auth D] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain X [auth F] MOL2 format, chain W [auth F] MOL2 format, chain U [auth E] MOL2 format, chain T [auth E] MOL2 format, chain R [auth D] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain X [auth F] mmCIF format, chain W [auth F] mmCIF format, chain U [auth E] mmCIF format, chain T [auth E] mmCIF format, chain R [auth D] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] K [auth B] L [auth B] N [auth C] H [auth A], I [auth A], K [auth B], L [auth B], N [auth C], O [auth C], Q [auth D], R [auth D], T [auth E], U [auth E], W [auth F], X [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain W [auth F] Focus chain X [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain W [auth F] Focus chain X [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free: 0.271 (Depositor), 0.271 (DCC)
R-Value Work: 0.227 (Depositor), 0.227 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.623	α = 90
b = 69.081	β = 97.39
c = 154.987	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-25

Deposition Author(s):

Yehia, R.

Giladi, M.

Haitin, Y.

Funding Organization	Location	Grant Number
Israel Science Foundation	Israel	1653/21
Israel Science Foundation	Israel	1721/16
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