SAXSdb — 4pvx

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

Farnesyl 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 2	MAGNESIUM ION × 6 [({4-[4-(cyclopropyloxy)phenyl]pyridin-2-yl}amino)methanediyl]bis(phosphonic acid) × 2 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FPPS_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain F； PDBConstruct 23–375； UniProt 67–419

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	4pvx
Deposition date deposition_date	2014-03-18
Structure title title	Crystal structure of human FPPS in complex with [({4-[4-(cyclopropyloxy)phenyl]pyridin-2-yl}amino)methanediyl]bis(phosphonic acid)
Keywords keywords	Transferase-transferase inhibitor complex; Transferase/transferase inhibitor
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.

4pvx__assembly_1__model_1

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

Download this curve (.dat)

4pvx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4pvx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.26 Å
Rg (electron density)	26.35 Å
Total Rg	27.16 Å
Atom count	5572
Residues	686
Excluded volume	99806 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4pvx__assembly_1__model_1`	dimeric （2）	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 (5)

Entity 1 Entity 1 polymer

Description description	Farnesyl pyrophosphate synthase
Molecular weight formula_weight	43145.0 kDa
EC 编号 ec_number	2.5.1.10, 2.5.1.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F
Atom count atom_count	2948

MGSSHHHHHHSSGRENLYFQGHMNGDQNSDVYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGKYNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYKRRK

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	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	[({4-[4-(cyclopropyloxy)phenyl]pyridin-2-yl}amino)methanediyl]bis(phosphonic acid)
Molecular weight formula_weight	400.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	148

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4pvxf_
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 (1 domains)

Domain ID domain_id	4pvxF00
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	111.260 Å
Unit-cell length b length_b	111.260 Å
Unit-cell length c length_c	69.340 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.180 Å
Low-resolution limit resolution_low	69.340 Å
R factor r_factor	0.1723
R_work r_work	0.1697
R_free r_free	0.2201

Crystal structure of human FPPS in complex with [({4-[4-(cyclopropyloxy)phenyl]pyridin-2-yl}amino)methanediyl]bis(phosphonic acid)

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

Farnesyl 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

4pvx__assembly_1__model_1

4pvx__assembly_1__model_1 | I(q)

4pvx__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of human FPPS in complex with [({4-[4-(cyclopropyloxy)phenyl]pyridin-2-yl}amino)methanediyl]bis(phosphonic acid)

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

Farnesyl 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

4pvx__assembly_1__model_1

4pvx__assembly_1__model_1 | I(q)

4pvx__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)