SAXSdb — 3vdk

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

Circumsporozoite (CS) protein

Plasmodium falciparum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	PLATINUM (II) ION × 1 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	PLATINUM (II) ION × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7K740_PLAF7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–69； UniProt 310–374

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	3vdk
Deposition date deposition_date	2012-01-05
Structure title title	Crystal structure of circumsporozoite protein aTSR domain, R32 platinum-bound form
Keywords keywords	TSR, aTSR, CELL INVASION; CELL INVASION
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.

3vdk__assembly_1__model_1

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

Download this curve (.dat)

3vdk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3vdk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.55 Å
Rg (electron density)	13.56 Å
Total Rg	14.65 Å
Atom count	568
Residues	71
Excluded volume	10116 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3vdk__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3vdk__assembly_2__model_1`	trimeric （3）	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	Circumsporozoite (CS) protein
Molecular weight formula_weight	8902.1 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	620

YVEFEPSDKHIKEYLNKIQNSLSTEWSPCSVTCGNGIQVRIKPGSANKPKDELDYANDIEKKICKMEKCPHHHHHHA

Source Source

Source organism organism	Plasmodium falciparum
NCBI taxonomy ID ncbi_taxonomy_id	36329
Host organism host_organism	Pichia pastoris

Entity 2 Entity 2 non-polymer

Description description	PLATINUM (II) ION
Molecular weight formula_weight	195.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	52

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3vdkA00
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	100 — TSP-1 type 1 repeat
Homologous superfamily homologous superfamily	10 — Thrombospondin type-1 (TSP1) repeat

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Unit-cell length a length_a	66.534 Å
Unit-cell length b length_b	66.534 Å
Unit-cell length c length_c	86.488 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	1.847 Å
Low-resolution limit resolution_low	33.267 Å
R factor r_factor	0.1800
R_work r_work	0.1759
R_free r_free	0.2168

Crystal structure of circumsporozoite protein aTSR domain, R32 platinum-bound form

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

Circumsporozoite (CS) protein

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

3vdk__assembly_1__model_1

3vdk__assembly_1__model_1 | I(q)

3vdk__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of circumsporozoite protein aTSR domain, R32 platinum-bound form

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

Circumsporozoite (CS) protein

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

3vdk__assembly_1__model_1

3vdk__assembly_1__model_1 | I(q)

3vdk__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)