6g31

Crystal structure of human geranylgeranyl diphosphate synthase mutant D188Y bound to zoledronate

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Geranylgeranyl pyrophosphate synthase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	ZOLEDRONIC ACID × 6 MAGNESIUM ION × 18	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	ZOLEDRONIC ACID × 6 MAGNESIUM ION × 18	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GGPPS_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–307； UniProt 1–300 Author chain B； PDBConstruct 8–307； UniProt 1–300 Author chain C； PDBConstruct 8–307； UniProt 1–300 Author chain D； PDBConstruct 8–307； UniProt 1–300 Author chain E； PDBConstruct 8–307； UniProt 1–300 Author chain F； PDBConstruct 8–307； UniProt 1–300 Author chain G； PDBConstruct 8–307； UniProt 1–300 Author chain H； PDBConstruct 8–307； UniProt 1–300 Author chain I； PDBConstruct 8–307； UniProt 1–300 Author chain J； PDBConstruct 8–307； UniProt 1–300 Author chain K； PDBConstruct 8–307； UniProt 1–300 Author chain L； PDBConstruct 8–307； UniProt 1–300

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6g31
Deposition date deposition_date	2018-03-24
Structure title title	Crystal structure of human geranylgeranyl diphosphate synthase mutant D188Y bound to zoledronate
Keywords keywords	geranylgeranyl diphosphate synthase, mevalonate pathway, prenyltransferase, GGPPS, bisphosphonates, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6g31__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6g31__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6g31__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	39.55 Å
Rg (electron density)	38.97 Å
Total Rg	39.17 Å
Atom count	11833
Residues	1682
Excluded volume	206420 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6g31__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6g31__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Geranylgeranyl pyrophosphate synthase
Molecular weight formula_weight	35484.4 kDa
EC 编号 ec_number	2.5.1.-,2.5.1.1,2.5.1.29,2.5.1.10
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	23597

GSGSGSGMEKTQETVQRILLEPYKYLLQLPGKQVRTKLSQAFNHWLKVPEDKLQIIIEVTEMLHNASLLIDDIEDNSKLRRGFPVAHSIYGIPSVINSANYVYFLGLEKVLTLDHQDAVKLFTRQLLELHQGQGLDIYWRDNYTCPTEEEYKAMVLQKTGGLFGLAVGLMQLFSDYKEDLKPLLNTLGLFFQIRYDYANLHSKEYSENKSFCEDLTEGKFSFPTIHAIWSRPESTQVQNILRQRTENIDIKKYCVHYLEDVGSFEYTRNTLKELEAKAYKQIDARGGNPELVALVKHLSKMFKEENE

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZOLEDRONIC ACID
Molecular weight formula_weight	272.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	36

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d6g31a_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.1 — Isoprenyl diphosphate synthases

Domain ID domain_id	d6g31b_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.1 — Isoprenyl diphosphate synthases

Domain ID domain_id	d6g31c_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.1 — Isoprenyl diphosphate synthases

Domain ID domain_id	d6g31d_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.1 — Isoprenyl diphosphate synthases

Domain ID domain_id	d6g31e_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.1 — Isoprenyl diphosphate synthases

Domain ID domain_id	d6g31f_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.1 — Isoprenyl diphosphate synthases

Domain ID domain_id	d6g31g_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.1 — Isoprenyl diphosphate synthases

Domain ID domain_id	d6g31h_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.1 — Isoprenyl diphosphate synthases

Domain ID domain_id	d6g31i_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.1 — Isoprenyl diphosphate synthases

Domain ID domain_id	d6g31j_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.1 — Isoprenyl diphosphate synthases

Domain ID domain_id	d6g31k_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.1 — Isoprenyl diphosphate synthases

Domain ID domain_id	d6g31l_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.1 — Isoprenyl diphosphate synthases

CATH v4.4 (12 domains)

Domain ID domain_id	6g31A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

Domain ID domain_id	6g31B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

Domain ID domain_id	6g31C00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

Domain ID domain_id	6g31D00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

Domain ID domain_id	6g31E00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

Domain ID domain_id	6g31F00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

Domain ID domain_id	6g31G00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

Domain ID domain_id	6g31H00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

Domain ID domain_id	6g31I00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

Domain ID domain_id	6g31J00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

Domain ID domain_id	6g31K00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

Domain ID domain_id	6g31L00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

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Unit-cell length a length_a	116.800 Å
Unit-cell length b length_b	134.240 Å
Unit-cell length c length_c	134.460 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.67 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	48.619 Å
R factor r_factor	0.2586
R_work r_work	0.2562
R_free r_free	0.3047

Crystal structure of human geranylgeranyl diphosphate synthase mutant D188Y bound to zoledronate

1. Protein Identity and Related Structures Protein Identity & Related Structures

Geranylgeranyl pyrophosphate synthase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6g31__assembly_2__model_1

6g31__assembly_2__model_1 | I(q)

6g31__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of human geranylgeranyl diphosphate synthase mutant D188Y bound to zoledronate

1. Protein Identity and Related Structures Protein Identity & Related Structures

Geranylgeranyl pyrophosphate synthase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6g31__assembly_2__model_1

6g31__assembly_2__model_1 | I(q)

6g31__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)