SAXSdb — 3rtj

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

Ricin A chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Homooligomer	Protein 2 RNA 1 其他Polymer 4	;RNA (5'-R(APG)-3') ; × 1 beta-D-galactopyranose-(1-4)-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2	Review required

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RICI_RICCO
Isoform	—
PDB entities	2, 3
Chains and sequence ranges	Author chain A； PDBConstruct 1–267； UniProt 36–302 Author chain B； PDBConstruct 1–262； UniProt 315–576

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	3rtj
Deposition date deposition_date	2011-05-03
Structure title title	Crystal structure of ricin bound with dinucleotide ApG
Keywords keywords	;enzyme-substrate complex, glycosidase ribosome-inactivating protein lectin glycoprotein, lactose binding, glycosylation, HYDROLASE, HYDROLASE-RNA complex ;; HYDROLASE/RNA
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.

3rtj__assembly_1__model_1

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

Download this curve (.dat)

3rtj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3rtj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.20 Å
Rg (electron density)	25.27 Å
Total Rg	25.96 Å
Atom count	4189
Residues	522
Excluded volume	73984 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3rtj__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	;RNA (5'-R(APG)-3') ;
Molecular weight formula_weight	629.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D
Atom count atom_count	4189

AG

Entity 2 Entity 2 polymer

Description description	Ricin A chain
Molecular weight formula_weight	29936.8 kDa
EC 编号 ec_number	3.2.2.22
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

IFPKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPPSSQF

Entity 3 Entity 3 polymer

Description description	Ricin B chain
Molecular weight formula_weight	28989.6 kDa
EC 编号 ec_number	3.2.2.22
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ADVCMDPEPIVRIVGRNGLCVDVRDGRFHNGNAIQLWPCKSNTDANQLWTLKRDNTIRSNGKCLTTYGYSPGVYVMIYDCNTAATDATRWQIWDNGTIINPRSSLVLAATSGNSGTTLTVQTNIYAVSQGWLPTNNTQPFVTTIVGLYGLCLQANSGQVWIEDCSSEKAEQQWALYADGSIRPQQNRDNCLTSDSNIRETVVKILSCGPASSGQRWMFKNDGTILNLYSGLVLDVRASDPSLKQIILYPLHGDPNQIWLPLF

Entity 4 Entity 4 branched

Description description	beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3rtja_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.165 — Ribosome inactivating proteins (RIP)
Superfamily Superfamily superfamily	d.165.1 — Ribosome inactivating proteins (RIP)
Family Family family	d.165.1.1 — Plant cytotoxins

Domain ID domain_id	d3rtjb1
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.0 — automated matches

Domain ID domain_id	d3rtjb2
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	3rtjA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	420 — Ricin (A subunit); domain 1
Homologous superfamily homologous superfamily	10 — Ricin (A subunit), domain 1

Domain ID domain_id	3rtjA02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily	10 — Ricin (A Subunit), domain 2

Domain ID domain_id	3rtjB01
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	3rtjB02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	72.740 Å
Unit-cell length b length_b	78.490 Å
Unit-cell length c length_c	114.340 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	19.910 Å
R factor r_factor	—
R_work r_work	0.1980
R_free r_free	—

Crystal structure of ricin bound with dinucleotide ApG

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

Ricin A 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

3rtj__assembly_1__model_1

3rtj__assembly_1__model_1 | I(q)

3rtj__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 polymer

Polymer Polymer

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of ricin bound with dinucleotide ApG

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

Ricin A 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

3rtj__assembly_1__model_1

3rtj__assembly_1__model_1 | I(q)

3rtj__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 polymer

Polymer Polymer

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)