1vcl

Crystal Structure of Hemolytic Lectin CEL-III

Method: X-RAY DIFFRACTION

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

hemolytic lectin CEL-III

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CALCIUM ION × 5 MAGNESIUM ION × 2 CHLORIDE ION × 1 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CALCIUM ION × 5 MAGNESIUM ION × 2 CHLORIDE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q868M7_9ECHN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–432； UniProt 11–442 Author chain B； PDBConstruct 1–432； UniProt 11–442

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	1vcl
Deposition date deposition_date	2004-03-09
Structure title title	Crystal Structure of Hemolytic Lectin CEL-III
Keywords keywords	LECTIN, CEL-III, HEMOLYSIS, HEMAGGLUTINATION, PORE-FORMING, CALCIUM, toxin; TOXIN
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.

1vcl__assembly_1__model_1

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

Download this curve (.dat)

1vcl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vcl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.77 Å
Rg (electron density)	22.73 Å
Total Rg	23.53 Å
Atom count	3335
Residues	431
Excluded volume	58342 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vcl__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1vcl__assembly_2__model_1`	monomeric （1）	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	hemolytic lectin CEL-III
Molecular weight formula_weight	47452.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7502

QVLCTNPLDIGELRSFKSKQCVDIVGNQGSGNIATYDCDGLSDQQIIICGDGTIRNEARNYCFTPDGSGNANVMSSPCTLYPEIPSSQRWRQGRRKTFTDNGGIEQVATEIINLASGKCLDIEGSDGTGDIGVYDCQNLDDQYFYVRSRGPELFYGRLRNEKSDLCLDVEGSDGKGNVLMYSCEDNLDQWFRYYENGEIVNAKSGMCLDVEGSDGSGNVGIYRCDDLRDQMWSRPNAYCNGDYCSFLNKESNKCLDVSGDQGTGDVGTWQCDGLPDQRFKWVFDDWEVPTATWNMVGCDQNGKVSQQISNTISFSSTVTAGVAVEVSSTIEKGVIFAKATVSVKVTASLSKAWTNSQSGTTAITYTCDNYDSDEEFTRGCMWQLAIETTEVKSGDLLVWNPQIVKCTRSNTAPGCAPFTKCANEDCTFCTDI

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	209.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	846

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1vcla1
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.1 — Ricin B-like

Domain ID domain_id	d1vcla2
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.1 — Ricin B-like

Domain ID domain_id	d1vcla3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.281 — Hemolytic lectin CEL-III, C-terminal domain
Superfamily Superfamily superfamily	d.281.1 — Hemolytic lectin CEL-III, C-terminal domain
Family Family family	d.281.1.1 — Hemolytic lectin CEL-III, C-terminal domain

Domain ID domain_id	d1vclb1
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.1 — Ricin B-like

Domain ID domain_id	d1vclb2
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.1 — Ricin B-like

Domain ID domain_id	d1vclb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.281 — Hemolytic lectin CEL-III, C-terminal domain
Superfamily Superfamily superfamily	d.281.1 — Hemolytic lectin CEL-III, C-terminal domain
Family Family family	d.281.1.1 — Hemolytic lectin CEL-III, C-terminal domain

CATH v4.4 (6 domains)

Domain ID domain_id	1vclA01
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1vclA02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1vclA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1750 — hemolytic lectin cel-iii, domain 3
Homologous superfamily homologous superfamily	10 — Hemolytic lectin CEL-III, C-terminal domain

Domain ID domain_id	1vclB01
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1vclB02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1vclB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1750 — hemolytic lectin cel-iii, domain 3
Homologous superfamily homologous superfamily	10 — Hemolytic lectin CEL-III, C-terminal domain

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Unit-cell length a length_a	52.420 Å
Unit-cell length b length_b	65.370 Å
Unit-cell length c length_c	126.020 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.18 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	26.170 Å
R factor r_factor	0.1670
R_work r_work	0.1652
R_free r_free	0.2012

Crystal Structure of Hemolytic Lectin CEL-III

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

hemolytic lectin CEL-III

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

1vcl__assembly_1__model_1

1vcl__assembly_1__model_1 | I(q)

1vcl__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

Entity 2 Entity 2 non-polymer

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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structure of Hemolytic Lectin CEL-III

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

hemolytic lectin CEL-III

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

1vcl__assembly_1__model_1

1vcl__assembly_1__model_1 | I(q)

1vcl__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

Entity 2 Entity 2 non-polymer

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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)