2d04

Crystal structure of neoculin, a sweet protein with taste-modifying activity.

Method: X-RAY DIFFRACTION

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

Curculin

OrganismNot specified

UniProt P19667

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	neoculin acidic subunit × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	neoculin acidic subunit × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	neoculin acidic subunit × 1 water × 2	Consistent with protein count
4	Other combination	Heteromer	Protein 2 其他Polymer 1	neoculin acidic subunit × 1 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CURC_CURLA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–114； UniProt 23–136 Author chain D； PDBConstruct 1–114； UniProt 23–136 Author chain F； PDBConstruct 1–114； UniProt 23–136 Author chain H； PDBConstruct 1–114； UniProt 23–136

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	2d04
Deposition date deposition_date	2005-07-25
Structure title title	Crystal structure of neoculin, a sweet protein with taste-modifying activity.
Keywords keywords	all beta, 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.

2d04__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2d04__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2d04__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	19.74 Å
Rg (electron density)	18.37 Å
Total Rg	19.23 Å
Atom count	1710
Residues	221
Excluded volume	29938 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2d04__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2d04__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2d04__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2d04__assembly_4__model_1`	dimeric （2）	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	neoculin acidic subunit
Molecular weight formula_weight	12408.8 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	7112

DSVLLSGQTLYAGHSLTSGSYTLTIQNNCNLVKYQHGRQIWASDTDGQGSQCRLTLRSDGNLIIYDDNNMVVWGSDCWGNNGTYALVLQQDGLFVIYGPVLWPLGLNGCRSLN

Entity 2 Entity 2 polymer

Description description	Curculin
Molecular weight formula_weight	12593.1 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

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

DNVLLSGQTLHADHSLQAGAYTLTIQNKCNLVKYQNGRQIWASNTDRRGSGCRLTLLSDGNLVIYDHNNNDVWGSACWGDNGKYALVLQKDGRFVIYGPVLWSLGPNGCRRVNG

Entity 3 Entity 3 branched

Description description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	732.7 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	165

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2d04a_
Class class	b — All beta proteins
Fold Fold fold	b.78 — beta-Prism II
Superfamily Superfamily superfamily	b.78.1 — alpha-D-mannose-specific plant lectins
Family Family family	b.78.1.0 — automated matches

Domain ID domain_id	d2d04b_
Class class	b — All beta proteins
Fold Fold fold	b.78 — beta-Prism II
Superfamily Superfamily superfamily	b.78.1 — alpha-D-mannose-specific plant lectins
Family Family family	b.78.1.0 — automated matches

Domain ID domain_id	d2d04c_
Class class	b — All beta proteins
Fold Fold fold	b.78 — beta-Prism II
Superfamily Superfamily superfamily	b.78.1 — alpha-D-mannose-specific plant lectins
Family Family family	b.78.1.0 — automated matches

Domain ID domain_id	d2d04d_
Class class	b — All beta proteins
Fold Fold fold	b.78 — beta-Prism II
Superfamily Superfamily superfamily	b.78.1 — alpha-D-mannose-specific plant lectins
Family Family family	b.78.1.0 — automated matches

Domain ID domain_id	d2d04e_
Class class	b — All beta proteins
Fold Fold fold	b.78 — beta-Prism II
Superfamily Superfamily superfamily	b.78.1 — alpha-D-mannose-specific plant lectins
Family Family family	b.78.1.0 — automated matches

Domain ID domain_id	d2d04f_
Class class	b — All beta proteins
Fold Fold fold	b.78 — beta-Prism II
Superfamily Superfamily superfamily	b.78.1 — alpha-D-mannose-specific plant lectins
Family Family family	b.78.1.0 — automated matches

Domain ID domain_id	d2d04g_
Class class	b — All beta proteins
Fold Fold fold	b.78 — beta-Prism II
Superfamily Superfamily superfamily	b.78.1 — alpha-D-mannose-specific plant lectins
Family Family family	b.78.1.0 — automated matches

Domain ID domain_id	d2d04h_
Class class	b — All beta proteins
Fold Fold fold	b.78 — beta-Prism II
Superfamily Superfamily superfamily	b.78.1 — alpha-D-mannose-specific plant lectins
Family Family family	b.78.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	2d04A00
Class class	2 — Mainly Beta
Architecture architecture	90 — Orthogonal Prism
Topology topology	10 — Agglutinin, subunit A
Homologous superfamily homologous superfamily	10 — Bulb-type lectin domain

Domain ID domain_id	2d04B00
Class class	2 — Mainly Beta
Architecture architecture	90 — Orthogonal Prism
Topology topology	10 — Agglutinin, subunit A
Homologous superfamily homologous superfamily	10 — Bulb-type lectin domain

Domain ID domain_id	2d04C00
Class class	2 — Mainly Beta
Architecture architecture	90 — Orthogonal Prism
Topology topology	10 — Agglutinin, subunit A
Homologous superfamily homologous superfamily	10 — Bulb-type lectin domain

Domain ID domain_id	2d04D00
Class class	2 — Mainly Beta
Architecture architecture	90 — Orthogonal Prism
Topology topology	10 — Agglutinin, subunit A
Homologous superfamily homologous superfamily	10 — Bulb-type lectin domain

Domain ID domain_id	2d04E00
Class class	2 — Mainly Beta
Architecture architecture	90 — Orthogonal Prism
Topology topology	10 — Agglutinin, subunit A
Homologous superfamily homologous superfamily	10 — Bulb-type lectin domain

Domain ID domain_id	2d04F00
Class class	2 — Mainly Beta
Architecture architecture	90 — Orthogonal Prism
Topology topology	10 — Agglutinin, subunit A
Homologous superfamily homologous superfamily	10 — Bulb-type lectin domain

Domain ID domain_id	2d04G00
Class class	2 — Mainly Beta
Architecture architecture	90 — Orthogonal Prism
Topology topology	10 — Agglutinin, subunit A
Homologous superfamily homologous superfamily	10 — Bulb-type lectin domain

Domain ID domain_id	2d04H00
Class class	2 — Mainly Beta
Architecture architecture	90 — Orthogonal Prism
Topology topology	10 — Agglutinin, subunit A
Homologous superfamily homologous superfamily	10 — Bulb-type lectin domain

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Unit-cell length a length_a	48.009 Å
Unit-cell length b length_b	101.089 Å
Unit-cell length c length_c	271.572 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.760 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2450
R_work r_work	0.2450
R_free r_free	0.2670

Crystal structure of neoculin, a sweet protein with taste-modifying activity.

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

Curculin

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

2d04__assembly_3__model_1

2d04__assembly_3__model_1 | I(q)

2d04__assembly_3__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 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of neoculin, a sweet protein with taste-modifying activity.

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

Curculin

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

2d04__assembly_3__model_1

2d04__assembly_3__model_1 | I(q)

2d04__assembly_3__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 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)