SAXSdb — 5xfi

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

Lectin

Calystegia sepium

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 2 其他Polymer 2	;beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 SULFATE ION × 4 1,2-ETHANEDIOL × 2 BENZOIC ACID × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P93114_CALSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–153； UniProt 1–153 Author chain B； PDBConstruct 1–153； UniProt 1–153

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	5xfi
Deposition date deposition_date	2017-04-10
Structure title title	Crystal structure of Calsepa lectin in complex with biantennary N-glycan
Keywords keywords	Lectin, Jacalin-related lectin, N-glycan, Glycobiology, SUGAR BINDING PROTEIN; SUGAR BINDING 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.

5xfi__assembly_1__model_1

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

Download this curve (.dat)

5xfi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5xfi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.73 Å
Rg (electron density)	19.75 Å
Total Rg	20.66 Å
Atom count	2498
Residues	304
Excluded volume	43983 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5xfi__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Description description	Lectin
Molecular weight formula_weight	16074.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2630

MAVPMDTISGPWGNNGGNFWSFRPVNKINQIVISYGGGGNNPIALTFSSTKADGSKDTITVGGGGPDSITGTEMVNIGTDEYLTGISGTFGIYLDNNVLRSITFTTNLKAHGPYGQKVGTPFSSANVVGNEIVGFLGRSGYYVDAIGTYNRHK

Source Source

Source organism organism	Calystegia sepium
Common name common_name	Hedge bindweed
NCBI taxonomy ID ncbi_taxonomy_id	47519
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	;beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1479.3 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	BENZOIC ACID
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	132

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5xfia_
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	d5xfib_
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 (2 domains)

Domain ID domain_id	5xfiA00
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	5xfiB00
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	37.985 Å
Unit-cell length b length_b	37.985 Å
Unit-cell length c length_c	199.911 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	8

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	1.653 Å
Low-resolution limit resolution_low	35.508 Å
R factor r_factor	0.1893
R_work r_work	0.1877
R_free r_free	0.2204

Crystal structure of Calsepa lectin in complex with biantennary N-glycan

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

Lectin

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

5xfi__assembly_1__model_1

5xfi__assembly_1__model_1 | I(q)

5xfi__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Calsepa lectin in complex with biantennary N-glycan

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

Lectin

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

5xfi__assembly_1__model_1

5xfi__assembly_1__model_1 | I(q)

5xfi__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)