SAXSdb — 3rbm

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

Farnesyl pyrophosphate synthase

Plasmodium vivax

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 3-(2,2-diphosphonoethyl)-1-dodecyl-1H-imidazol-3-ium × 2 SULFATE ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 6 3-(2,2-diphosphonoethyl)-1-dodecyl-1H-imidazol-3-ium × 2 SULFATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A5K4U6_PLAVS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–396； UniProt 1–375 Author chain B； PDBConstruct 22–396； UniProt 1–375 Author chain C； PDBConstruct 22–396； UniProt 1–375 Author chain D； PDBConstruct 22–396； UniProt 1–375

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	3rbm
Deposition date deposition_date	2011-03-29
Structure title title	Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with BPH -703
Keywords keywords	ALPHA-HELICES, ISOPRENE BIOSYNTHESIS, 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.

3rbm__assembly_2__model_1

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

Download this curve (.dat)

3rbm__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3rbm__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	27.34 Å
Rg (electron density)	26.45 Å
Total Rg	27.29 Å
Atom count	5863
Residues	713
Excluded volume	105750 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3rbm__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3rbm__assembly_2__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	46215.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	12025

MGSSHHHHHHSSGRENLYFQGMKETNSEEADSGLAFFRNMYDKYRDAFLSHLNEYSLEEEIKEHISKYYKLLFDYNCLGGKNNRGILVILIYEYVKNRDINSSEWEKAACLAWCIEILQAAFLVADDIMDKGEMRRNKYCWYLLKDVETKNAVNDVLLLYNSIYKLIEIYLRNESCYVDVIATFRDATLKTIIGQHLDTNIFSDKYSDAHREIDVNNINVPEQPVIDINMINFGVYKNIVIHKTAYYSFFLPIVCGMLLAGIAVDNLIYKKIEDISMLMGEYFQIHDDYLDIFGDSTKTGKVGSDIQNNKLTWPLIKTFELCSEPDKIKIVKNYGKNNLACVKVIDSLYEQYKIRKHYESYEKAQKAKILSAINELHHEGIEYVLKYLLEILFTGV

Source Source

Source organism organism	Plasmodium vivax
NCBI taxonomy ID ncbi_taxonomy_id	126793
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	12

Entity 3 Entity 3 non-polymer

Description description	3-(2,2-diphosphonoethyl)-1-dodecyl-1H-imidazol-3-ium
Molecular weight formula_weight	425.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	266

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3rbmA00
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	3rbmB00
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	3rbmC00
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	3rbmD00
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	107.682 Å
Unit-cell length b length_b	107.952 Å
Unit-cell length c length_c	140.703 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.610 Å
Low-resolution limit resolution_low	45.580 Å
R factor r_factor	0.2100
R_work r_work	0.2080
R_free r_free	0.2530

Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with BPH -703

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

3rbm__assembly_2__model_1

3rbm__assembly_2__model_1 | I(q)

3rbm__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 (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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with BPH -703

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

3rbm__assembly_2__model_1

3rbm__assembly_2__model_1 | I(q)

3rbm__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 (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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)