1dgr

Refined crystal structure of canavalin from jack bean

Method: X-RAY DIFFRACTION

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

CANAVALIN

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 9	PHOSPHATE ION × 3 water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CANA_CANEN
Isoform	—
PDB entities	1, 2, 3
Chains and sequence ranges	Author chain A； PDBConstruct 1–178； UniProt 46–223 Author chain B； PDBConstruct 1–178； UniProt 46–223 Author chain C； PDBConstruct 1–178； UniProt 46–223 Author chain N； PDBConstruct 1–79； UniProt 246–324 Author chain V； PDBConstruct 1–79； UniProt 246–324 Author chain X； PDBConstruct 1–79； UniProt 246–324 Author chain M； PDBConstruct 1–93； UniProt 331–423 Author chain W； PDBConstruct 1–93； UniProt 331–423 Author chain Y； PDBConstruct 1–93； UniProt 331–423

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	1dgr
Deposition date deposition_date	1999-11-25
Structure title title	Refined crystal structure of canavalin from jack bean
Keywords keywords	DUPLICATED DOMAINS BETA BARREL HELICAL LOOP, PLANT PROTEIN; PLANT 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.

1dgr__assembly_1__model_1

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

Download this curve (.dat)

1dgr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1dgr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.74 Å
Rg (electron density)	32.59 Å
Total Rg	33.18 Å
Atom count	8362
Residues	1039
Excluded volume	148400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1dgr__assembly_1__model_1`	nonameric （9）	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	CANAVALIN
Molecular weight formula_weight	20640.3 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	8530

NNPYLFRSNKFLTLFKNQHGSLRLLQRFNEDTEKLENLRDYRVLEYCSKPNTLLLPHHSDSDLLVLVLEGQAILVLVNPDGRDTYKLDQGDAIKIQAGTPFYLINPDNNQNLRILKFAITFRRPGTVEDFFLSSTKRLPSYLSAFSKNFLEASYDSPYDEIEQTLLQEEQEGVIVKMP

Entity 2 Entity 2 polymer

Description description	CANAVALIN
Molecular weight formula_weight	9073.2 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X,V,N

DKPFNLRSRDPIYSNNYGKLYEITPEKNSQLRDLDILLNCLQMNEGALFVPHYNSRATVILVANEGRAEVELVGLEQQQ

Entity 3 Entity 3 polymer

Description description	CANAVALIN
Molecular weight formula_weight	10269.4 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y,W,M

MQLRRYAATLSEGDIIVIPSSFPVALKAASDLNMVGIGVNAENNERNFLAGHKENVIRQIPRQVSDLTFPGSGEEVEELLENQKESYFVDGQP

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	168

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1dgr.1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.2 — Germin/Seed storage 7S protein

Domain ID domain_id	d1dgr.2
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.2 — Germin/Seed storage 7S protein

Domain ID domain_id	d1dgr.4
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.2 — Germin/Seed storage 7S protein

Domain ID domain_id	d1dgra_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.2 — Germin/Seed storage 7S protein

Domain ID domain_id	d1dgrb_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.2 — Germin/Seed storage 7S protein

Domain ID domain_id	d1dgrc_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.2 — Germin/Seed storage 7S protein

CATH v4.4 (9 domains)

Domain ID domain_id	1dgrA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	1dgrB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	1dgrC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	1dgrM01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	840 —

Domain ID domain_id	1dgrN00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1450 —

Domain ID domain_id	1dgrV00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1450 —

Domain ID domain_id	1dgrW01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	840 —

Domain ID domain_id	1dgrX00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1450 —

Domain ID domain_id	1dgrY01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	840 —

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Unit-cell length a length_a	136.500 Å
Unit-cell length b length_b	150.300 Å
Unit-cell length c length_c	133.400 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	24

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	200.000 Å
R factor r_factor	0.1840
R_work r_work	0.1800
R_free r_free	0.2260

Refined crystal structure of canavalin from jack bean

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

CANAVALIN

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

1dgr__assembly_1__model_1

1dgr__assembly_1__model_1 | I(q)

1dgr__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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

7. Citations (2)

Refined crystal structure of canavalin from jack bean

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

CANAVALIN

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

1dgr__assembly_1__model_1

1dgr__assembly_1__model_1 | I(q)

1dgr__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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

7. Citations (2)