SAXSdb — 4lv8

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

Rhoptry protein 5 C

Toxoplasma gondii type I

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Interferon-inducible GTPase 1 × 1 （Q9QZ85） ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 1,2-ETHANEDIOL × 10 GUANOSINE-5'-DIPHOSPHATE × 1 water × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 1,2-ETHANEDIOL × 5 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	I6ZQR7_TOXGO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–371； UniProt 175–541

Interferon-inducible GTPase 1

Mus musculus

UniProt Q9QZ85

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Rhoptry protein 5 C × 1 （I6ZQR7） ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 1,2-ETHANEDIOL × 10 GUANOSINE-5'-DIPHOSPHATE × 1 water × 2	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	1,2-ETHANEDIOL × 5 GUANOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IIGP1_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 11–423； UniProt 1–413

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	4lv8
Deposition date deposition_date	2013-07-26
Structure title title	Murine IRGa6 bound to Toxoplasma ROP5C, a pseudokinase GDI
Keywords keywords	immune related GTPase, guanine dissociation inhibitor, parasite effector, Transferase-Hydrolase complex; Transferase/Hydrolase
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.

4lv8__assembly_1__model_1

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

Download this curve (.dat)

4lv8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4lv8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.99 Å
Rg (electron density)	35.12 Å
Total Rg	35.36 Å
Atom count	6087
Residues	750
Excluded volume	109220 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4lv8__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4lv8__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4lv8__assembly_3__model_1`	monomeric （1）	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 (7)

Entity 1 Entity 1 polymer

Description description	Rhoptry protein 5 C
Molecular weight formula_weight	41347.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6676

GSHMEAGDSFMRDLLKREEELIGYCREEALKEPAAMVEAVTATVWPQNAETTVDSLLSQGERKLKLVEPLRVGDRSVVFLVRDVERLEDFALKVFTMGAENSRSELERLHEATFAAARLLGESPEEARDRRRLLLPSDAVAVQSQPPFAQLSPGQSDYAVANYLLLMPAASVDLELLFRTLDFLYVLRSTEDFLALHILTAQLIRLAANLQSKGLVHGHFTPDNLFIMPDGRLMLGDVSVLRKVGTRGPASSVPVTYAPREFLNASTATFTHALDAWQLGLSIYRVWCLFLPFGLVTPGIKGSWKRPSLRVPGTDSLAFGSCTPLPDFVQTLIGRFLNFDRRRRLLPLEAMETPEFLQLQNEISSSLSTGQ

Source Source

Source organism organism	Toxoplasma gondii type I
NCBI taxonomy ID ncbi_taxonomy_id	1209525
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Interferon-inducible GTPase 1
Molecular weight formula_weight	48484.5 kDa
EC 编号 ec_number	3.6.5.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSPGIPGSTTMGQLFSSPKSDENNDLPSSFTGYFKKFNTGRKIISQEILNLIELRMRKGNIQLTNSAISDALKEIDSSVLNVAVTGETGSGKSSFINTLRGIGNEEEGAAKTGVVEVTMERHPYKHPNIPNVVFWDLPGIGSTNFPPNTYLEKMKFYEYDFFIIISATRFKKNDIDIAKAISMMKKEFYFVRTKVDSDITNEADGKPQTFDKEKVLQDIRLNCVNTFRENGIAEPPIFLLSNKNVCHYDFPVLMDKLISDLPIYKRHNFMVSLPNITDSVIEKKRQFLKQRIWLEGFAADLVNIIPSLTFLLDSDLETLKKSMKFYRTVFGVDETSLQRLARDWEIEVDQVEAMIKSPAVFKPTDEETIQERLSRYIQEFCLANGYLLPKNSFLKEIFYLKYYFLDMVTEDAKTLLKEICLRN

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 6 Entity 6 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	515

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4lv8b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

CATH v4.4 (3 domains)

Domain ID domain_id	4lv8A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	4lv8A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	4lv8B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	53.400 Å
Unit-cell length b length_b	53.700 Å
Unit-cell length c length_c	86.800 Å
Unit-cell angle α angle_alpha	104.70 °
Unit-cell angle β angle_beta	95.30 °
Unit-cell angle γ angle_gamma	111.00 °
Molecules per unit cell Z z_pdb	1

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

Resolution resolution	1.720 Å
Low-resolution limit resolution_low	38.669 Å
R factor r_factor	0.1957
R_work r_work	0.1951
R_free r_free	0.2298

Murine IRGa6 bound to Toxoplasma ROP5C, a pseudokinase GDI

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

Rhoptry protein 5 C

State in the Current Structure

Other States of the Same Protein in the Database

Interferon-inducible GTPase 1

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

4lv8__assembly_1__model_1

4lv8__assembly_1__model_1 | I(q)

4lv8__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Murine IRGa6 bound to Toxoplasma ROP5C, a pseudokinase GDI

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

Rhoptry protein 5 C

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Interferon-inducible GTPase 1

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

4lv8__assembly_1__model_1

4lv8__assembly_1__model_1 | I(q)

4lv8__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)