SAXSdb — 3gpr

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

Rhodocetin subunit alpha

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	Rhodocetin subunit beta × 1 （P81398） Rhodocetin subunit gamma × 1 Rhodocetin subunit delta × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RHCA_AGKRH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–133； UniProt 1–133

Rhodocetin subunit beta

OrganismNot specified

UniProt P81398

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Rhodocetin subunit alpha × 1 （P81397） Rhodocetin subunit gamma × 1 Rhodocetin subunit delta × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RHCB_AGKRH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–129； UniProt 1–129

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	3gpr
Deposition date deposition_date	2009-03-23
Structure title title	Crystal structure of rhodocetin
Keywords keywords	Rhodocetin, Disulfide bond, Lectin, Secreted, TOXIN, CELL ADHESION; CELL ADHESION
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.

3gpr__assembly_1__model_1

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

Download this curve (.dat)

3gpr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gpr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.00 Å
Rg (electron density)	26.16 Å
Total Rg	27.07 Å
Atom count	4295
Residues	517
Excluded volume	75847 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gpr__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	Rhodocetin subunit alpha
Molecular weight formula_weight	15983.0 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	4295

DCPDGWSSTKSYCYRPFKEKKTWEEAERFCTEQEKEAHLVSMENRLEAVFVDMVMENNFENKIYRSWIGLKIENKGQRSNLEWSDGSSISYENLYEPYMEKCFLMDHQSGLPKWHTADCEEKNVFMCKFQLPR

Entity 2 Entity 2 polymer

Description description	Rhodocetin subunit beta
Molecular weight formula_weight	15213.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DFRCPTTWSASKLYCYKPFKEKKTWIEAERFCAKQAENGHLVSIGSAAEADFLDLVIVVNFDKQRYRAWTGLTERNLKWTNGASVSYENLYEPYIRKCFVVQPWEGKSKWYKADCEEKNAFLCKFPKPH

Entity 3 Entity 3 polymer

Description description	Rhodocetin subunit gamma
Molecular weight formula_weight	15616.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

FNCLPGWSAYDQHCYQAFNEPKTWDEAERFCTEQAKRGHLVSIGSDGEADFVAQLVTNNIKRPELYVWIGLRDRRKEQQCSSEWSMSASIIYVNWNTGESQMCQGLARWTGFRKWDYSDCQAKNPFVCKFSSEC

Entity 4 Entity 4 polymer

Description description	Rhodocetin subunit delta
Molecular weight formula_weight	14737.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

CPLHWSSYNGYCYRVFSELKTWEDAESFCYAQHKGSRLASIHSREEEAFVGKLASQTLKYTSMWLGLNNAWAACKWEWSDDAKLDYKVWLRRAYCAVMVVKTDRIFWYNRGCEKTVSFLCKFYS

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3gprA00
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	3gprB00
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	3gprC00
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	3gprD00
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	83.546 Å
Unit-cell length b length_b	83.546 Å
Unit-cell length c length_c	196.078 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	6

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	29.780 Å
R factor r_factor	0.2230
R_work r_work	0.2230
R_free r_free	0.2840

Crystal structure of rhodocetin

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

Rhodocetin subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Rhodocetin subunit beta

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

3gpr__assembly_1__model_1

3gpr__assembly_1__model_1 | I(q)

3gpr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of rhodocetin

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

Rhodocetin subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Rhodocetin subunit beta

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

3gpr__assembly_1__model_1

3gpr__assembly_1__model_1 | I(q)

3gpr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)