SAXSdb — 9yio

▼

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

PvRipr EGF7-8

Plasmodium vivax

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	5B3 kappa chain × 1 5B3 heavy chain × 1 GLYCEROL × 3 SULFATE ION × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A564ZTL5_PLAVI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 4–83； UniProt 764–843

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9yio
Deposition date deposition_date	2025-10-02
Structure title title	Crystal structure of 5B3 Fab in complex with PvRipr EGF7-8
Keywords keywords	Plasmodium vivax, invasion, antibody-antigen complex, CELL INVASION; CELL INVASION
Experimental Method method	X-RAY DIFFRACTION

▼

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.

9yio__assembly_1__model_1

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

Download this curve (.dat)

9yio__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9yio__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.45 Å
Rg (electron density)	28.16 Å
Total Rg	28.98 Å
Atom count	3970
Residues	514
Excluded volume	70229 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9yio__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	PvRipr EGF7-8
Molecular weight formula_weight	9509.1 kDa
Mutation mutation	N767Q, N780Q
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	4214

GHMYCKQVTCKENEICKVVQNTPTCECKENLKRDSNNECVFNNMCLVNKGNCPIDSECIYHEKKRHQCLCHKKGLVAINGKCV

Source Source

Source organism organism	Plasmodium vivax
Common name common_name	malaria parasite P. vivax
NCBI taxonomy ID ncbi_taxonomy_id	5855
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	5B3 kappa chain
Molecular weight formula_weight	23237.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

QIVLSQSPAILSASPGEKVTMTCRASSSVNYMHWYQQKPGSSPKPWIYATSNLASGVPTRFSGSGSGTSYSLTISRVEAEDAATYYCQQWSPNPWTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNNRGE

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	5B3 heavy chain
Molecular weight formula_weight	24167.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

EVQVQQSGTELVRPGAVVKLSCIVSGFSIKDYYIHWVKQRPEKGLEWIGWIDPENGKTIYDPKFQGKASITADRSFNTAYLHISRPTSEDTAVYYCARSYYYGSSDAMDNWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Homo sapiens

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	3

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	238

▶

Unit-cell length a length_a	80.270 Å
Unit-cell length b length_b	81.746 Å
Unit-cell length c length_c	92.149 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	orthorhombic

Resolution resolution	2.080 Å
Low-resolution limit resolution_low	48.640 Å
R factor r_factor	0.2058
R_work r_work	0.2041
R_free r_free	0.2354

Crystal structure of 5B3 Fab in complex with PvRipr EGF7-8

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

PvRipr EGF7-8

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

9yio__assembly_1__model_1

9yio__assembly_1__model_1 | I(q)

9yio__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Crystal structure of 5B3 Fab in complex with PvRipr EGF7-8

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

PvRipr EGF7-8

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

9yio__assembly_1__model_1

9yio__assembly_1__model_1 | I(q)

9yio__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)