4kuc

Crystal structure of ricin-A chain in complex with the antibody 6C2

Method: X-RAY DIFFRACTION

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

Ricin

Ricinus communis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	mAb6c2 fab-Heavy chain × 1 mAb6c2 fab-Light chain × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	mAb6c2 fab-Heavy chain × 1 mAb6c2 fab-Light chain × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RICI_RICCO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–267； UniProt 36–302 Author chain I； PDBConstruct 1–267； UniProt 36–302

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	4kuc
Deposition date deposition_date	2013-05-21
Structure title title	Crystal structure of ricin-A chain in complex with the antibody 6C2
Keywords keywords	RNA-N-glycosidase, HYDROLASE-IMMUNE SYSTEM complex; HYDROLASE/IMMUNE SYSTEM
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.

4kuc__assembly_1__model_1

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

Download this curve (.dat)

4kuc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4kuc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.67 Å
Rg (electron density)	33.75 Å
Total Rg	34.08 Å
Atom count	4745
Residues	669
Excluded volume	83168 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4kuc__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4kuc__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	Ricin
Molecular weight formula_weight	29936.8 kDa
EC 编号 ec_number	3.2.2.22
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,I
Atom count atom_count	8287

IFPKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPPSSQF

Source Source

Source organism organism	Ricinus communis
Common name common_name	Castor bean
NCBI taxonomy ID ncbi_taxonomy_id	3988
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	mAb6c2 fab-Heavy chain
Molecular weight formula_weight	25401.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E

METDTLLLWVLLLWVPGSTGDIVLTQSPASLAVSLGQRATISYRASKSVSYMHWNQQKPGQPPRLLIYLGSNLESGVGARFSGSGSGTDFTLNIHPVEEEDAATYYCQHKREYPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVGNLQGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Mus musculus
NCBI taxonomy ID ncbi_taxonomy_id	10090

Entity 3 Entity 3 polymer

Description description	mAb6c2 fab-Light chain
Molecular weight formula_weight	25257.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,F

MGWSSIILFLVATASGVHSQVQLQQPGSELVRPGASVKLSCKASGYTFTSYWINWVKQRPGQGLEWIGNIYPGSGRTNYDEKFKNKATLTVDTSSSTVYIQVSSLTSEDAAVFYCVRWVYGNFDSALDYWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWGSGASGVHTFPAVLQSSGLYSLSSVVTVPSSSLGQTYICNVNHKPSNTKVDKKVEP

Source Source

Source organism organism	Mus musculus
NCBI taxonomy ID ncbi_taxonomy_id	10090

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6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d4kuca_
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	d4kucd1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d4kucd2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d4kuce_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d4kucf_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d4kuch_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d4kuci_
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

CATH v4.4 (10 domains)

Domain ID domain_id	4kucA01
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	4kucA02
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	4kucD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4kucD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4kucE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4kucF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4kucH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4kucH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4kucI01
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	4kucI02
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

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Unit-cell length a length_a	108.516 Å
Unit-cell length b length_b	151.803 Å
Unit-cell length c length_c	208.418 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	16

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.787 Å
Low-resolution limit resolution_low	36.436 Å
R factor r_factor	0.2409
R_work r_work	0.2384
R_free r_free	0.2889

Crystal structure of ricin-A chain in complex with the antibody 6C2

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

Ricin

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

4kuc__assembly_1__model_1

4kuc__assembly_1__model_1 | I(q)

4kuc__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (7 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Crystal structure of ricin-A chain in complex with the antibody 6C2

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

Ricin

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

4kuc__assembly_1__model_1

4kuc__assembly_1__model_1 | I(q)

4kuc__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (7 domains)

CATH v4.4 (10 domains)

7. Citations (1)