1vbo

Crystal structure of artocarpin-mannotriose complex

Method: X-RAY DIFFRACTION

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

artocarpin

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 4 其他Polymer 3	alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose × 3 alpha-D-mannopyranose × 1 water × 4	Consistent with protein count
2	Other combination	Homooligomer	Protein 4 其他Polymer 3	alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose × 3 alpha-D-mannopyranose × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7M1T4_ARTIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–147； UniProt 1–147 Author chain B； PDBConstruct 1–147； UniProt 1–147 Author chain C； PDBConstruct 1–147； UniProt 1–147 Author chain D； PDBConstruct 1–147； UniProt 1–147 Author chain E； PDBConstruct 1–147； UniProt 1–147 Author chain F； PDBConstruct 1–147； UniProt 1–147 Author chain G； PDBConstruct 1–147； UniProt 1–147 Author chain H； PDBConstruct 1–147； UniProt 1–147

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	1vbo
Deposition date deposition_date	2004-02-28
Structure title title	Crystal structure of artocarpin-mannotriose complex
Keywords keywords	beta-prism, mannose-specific, lectin, jacalin-like, 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.

1vbo__assembly_1__model_1

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

Download this curve (.dat)

1vbo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vbo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.03 Å
Rg (electron density)	27.22 Å
Total Rg	28.03 Å
Atom count	4678
Residues	592
Excluded volume	83249 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vbo__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1vbo__assembly_2__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	artocarpin
Molecular weight formula_weight	16113.0 kDa
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	9846

ASQTITVGPWGGPGGNGWDDGSYTGIRQIELSYKEAIGSFSVIYDLNGDPFSGPKHTSKLPYKNVKIELKFPDEFLESVSGYTGPFSALATPTPVVRSLTFKTNKGRTFGPYGDEEGTYFNLPIENGLIVGFKGRTGDLLDAIGIHMSL

Entity 2 Entity 2 branched

Description description	alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose
Molecular weight formula_weight	504.4 kDa
Source method src_method	man
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	alpha-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	490

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1vboa_
Class class	b — All beta proteins
Fold Fold fold	b.77 — beta-Prism I
Superfamily Superfamily superfamily	b.77.3 — Mannose-binding lectins
Family Family family	b.77.3.1 — Mannose-binding lectins

Domain ID domain_id	d1vbob_
Class class	b — All beta proteins
Fold Fold fold	b.77 — beta-Prism I
Superfamily Superfamily superfamily	b.77.3 — Mannose-binding lectins
Family Family family	b.77.3.1 — Mannose-binding lectins

Domain ID domain_id	d1vboc_
Class class	b — All beta proteins
Fold Fold fold	b.77 — beta-Prism I
Superfamily Superfamily superfamily	b.77.3 — Mannose-binding lectins
Family Family family	b.77.3.1 — Mannose-binding lectins

Domain ID domain_id	d1vbod_
Class class	b — All beta proteins
Fold Fold fold	b.77 — beta-Prism I
Superfamily Superfamily superfamily	b.77.3 — Mannose-binding lectins
Family Family family	b.77.3.1 — Mannose-binding lectins

Domain ID domain_id	d1vboe_
Class class	b — All beta proteins
Fold Fold fold	b.77 — beta-Prism I
Superfamily Superfamily superfamily	b.77.3 — Mannose-binding lectins
Family Family family	b.77.3.1 — Mannose-binding lectins

Domain ID domain_id	d1vbof_
Class class	b — All beta proteins
Fold Fold fold	b.77 — beta-Prism I
Superfamily Superfamily superfamily	b.77.3 — Mannose-binding lectins
Family Family family	b.77.3.1 — Mannose-binding lectins

Domain ID domain_id	d1vbog_
Class class	b — All beta proteins
Fold Fold fold	b.77 — beta-Prism I
Superfamily Superfamily superfamily	b.77.3 — Mannose-binding lectins
Family Family family	b.77.3.1 — Mannose-binding lectins

Domain ID domain_id	d1vboh_
Class class	b — All beta proteins
Fold Fold fold	b.77 — beta-Prism I
Superfamily Superfamily superfamily	b.77.3 — Mannose-binding lectins
Family Family family	b.77.3.1 — Mannose-binding lectins

CATH v4.4 (8 domains)

Domain ID domain_id	1vboA00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

Domain ID domain_id	1vboB00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

Domain ID domain_id	1vboC00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

Domain ID domain_id	1vboD00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

Domain ID domain_id	1vboE00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

Domain ID domain_id	1vboF00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

Domain ID domain_id	1vboG00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

Domain ID domain_id	1vboH00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

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Unit-cell length a length_a	138.217 Å
Unit-cell length b length_b	72.296 Å
Unit-cell length c length_c	59.373 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.48 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	19.850 Å
R factor r_factor	0.2090
R_work r_work	0.2090
R_free r_free	0.2260

Crystal structure of artocarpin-mannotriose complex

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

artocarpin

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

1vbo__assembly_1__model_1

1vbo__assembly_1__model_1 | I(q)

1vbo__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (4)

Crystal structure of artocarpin-mannotriose complex

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

artocarpin

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

1vbo__assembly_1__model_1

1vbo__assembly_1__model_1 | I(q)

1vbo__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (4)