SAXSdb — 2vrp

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

AGGRETIN ALPHA CHAIN

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	AGGRETIN BETA CHAIN × 2 （Q9I840） SODIUM ION × 8 CHLORIDE ION × 4 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	AGGRETIN BETA CHAIN × 2 （Q9I840） SODIUM ION × 8 CHLORIDE ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9I841_AGKRH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–136； UniProt 1–136

AGGRETIN BETA CHAIN

OrganismNot specified

UniProt Q9I840

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	AGGRETIN ALPHA CHAIN × 2 （Q9I841） SODIUM ION × 8 CHLORIDE ION × 4 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	AGGRETIN ALPHA CHAIN × 2 （Q9I841） SODIUM ION × 8 CHLORIDE ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9I840_AGKRH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–123； UniProt 24–146

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	2vrp
Deposition date deposition_date	2008-04-09
Structure title title	Structure of rhodocytin
Keywords keywords	C-TYPE LECTIN-LIKE, SUGAR-BINDING PROTEIN, LECTIN, CLEC-2, VENOM, AGGRETIN, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
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.

2vrp__assembly_1__model_1

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

Download this curve (.dat)

2vrp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vrp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.95 Å
Rg (electron density)	26.60 Å
Total Rg	27.32 Å
Atom count	4214
Residues	512
Excluded volume	73858 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vrp__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2vrp__assembly_2__model_1`	tetrameric （4）	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	AGGRETIN ALPHA CHAIN
Molecular weight formula_weight	15812.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2151

GLEDCDFGWSPYDQHCYQAFNEQKTWDEAEKFCRAQENGAHLASIESNGEADFVSWLISQKDELADEDYVWIGLRAQNKEQQCSSEWSDGSSVSYENLIDLHTKKCGALEKLTGFRKWVNYYCEQMHAFVCKLLPY

Entity 2 Entity 2 polymer

Description description	AGGRETIN BETA CHAIN
Molecular weight formula_weight	14388.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DCPSGWSSYEGHCYKPFNEPKNWADAERFCKLQPKHSHLVSFQSAEEADFVVKLTRPRLKANLVWMGLSNIWHGCNWQWSDGARLNYKDWQEQSECLAFRGVHTEWLNMDCSSTCSFVCKFKA

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	44

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2vrpa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d2vrpb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

CATH v4.4 (2 domains)

Domain ID domain_id	2vrpA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	2vrpB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

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Unit-cell length a length_a	61.933 Å
Unit-cell length b length_b	89.368 Å
Unit-cell length c length_c	120.996 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.410 Å
Low-resolution limit resolution_low	36.760 Å
R factor r_factor	0.2040
R_work r_work	0.2010
R_free r_free	0.2720

Structure of rhodocytin

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

AGGRETIN ALPHA CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

AGGRETIN BETA CHAIN

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

2vrp__assembly_1__model_1

2vrp__assembly_1__model_1 | I(q)

2vrp__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

Entity 2 Entity 2 polymer

Polymer 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

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of rhodocytin

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

AGGRETIN ALPHA CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

AGGRETIN BETA CHAIN

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

2vrp__assembly_1__model_1

2vrp__assembly_1__model_1 | I(q)

2vrp__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

Entity 2 Entity 2 polymer

Polymer 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

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)