2zr1

Agglutinin from Abrus Precatorius

Method: X-RAY DIFFRACTION

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

Agglutinin-1 chain A

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	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	AGGL_ABRPR
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–258； UniProt 21–278 Author chain C； PDBConstruct 1–258； UniProt 21–278 Author chain B； PDBConstruct 1–267； UniProt 281–547 Author chain D； PDBConstruct 1–267； UniProt 281–547

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	2zr1
Deposition date deposition_date	2008-08-22
Structure title title	Agglutinin from Abrus Precatorius
Keywords keywords	;RIBOSOME-INACTIVATING PROTEIN, IMMUNOTOXIN, AGGLUTININ ABRIN, Glycoprotein, Hydrolase, Lectin, Plant defense, Protein synthesis inhibitor, Pyrrolidone carboxylic acid, Toxin, 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.

2zr1__assembly_1__model_1

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

Download this curve (.dat)

2zr1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zr1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.77 Å
Rg (electron density)	24.87 Å
Total Rg	25.60 Å
Atom count	4058
Residues	513
Excluded volume	71931 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zr1__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2zr1__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	Agglutinin-1 chain A
Molecular weight formula_weight	28664.4 kDa
EC 编号 ec_number	3.2.2.22
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	8271

QDPIKFTTGSATPASYNQFIDALRERLTGGLIYGIPVLRDPSTVEKPNQYVTVELSYSDTVSIQLGIDLTNAYVVAYRAGSESFFFRNAPASASTYLFTGTQQYSLPFDGNYDDLEKWAHQSRQRISLGLEALRQGIKFLRSGASDDEEIARTLIVIIQMVAEAARFRYVSKLVVISLSNRAAFQPDPSMLSLENTWEPLSRAVQHTVQDTFPQNVTLINVRQERVVVSSLSHPSVSALALMLFVCNPLNATQSPLLI

Entity 2 Entity 2 polymer

Description description	Agglutinin-1 chain B
Molecular weight formula_weight	30006.8 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

VVEQSKICSSHYEPTVRIGGRDGLCVDVSDNAYNNGNPIILWKCKDQLEVNQLWTLKSDKTIRSKGKCLTTYGYAPGNYVMIYDCSSAVAEATYWDIWDNGTIINPKSGLVLSAESSSMGGTLTVQKNDYRMRQGWRTGNDTSPFVTSIAGFFKLCMEAHGNSMWLDVCDITKEEQQWAVYPDGSIRPVQNTNNCLTCEEHKQGATIVMMGCSNAWASQRWVFKSDGTIYNLYDDMVMDVKSSDPSLKQIILWPYTGNANQMWATLF

Entity 3 Entity 3 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	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	169

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2zr1a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.165 — Ribosome inactivating proteins (RIP)
Superfamily Superfamily superfamily	d.165.1 — Ribosome inactivating proteins (RIP)
Family Family family	d.165.1.1 — Plant cytotoxins

Domain ID domain_id	d2zr1b1
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	d2zr1b2
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	d2zr1c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.165 — Ribosome inactivating proteins (RIP)
Superfamily Superfamily superfamily	d.165.1 — Ribosome inactivating proteins (RIP)
Family Family family	d.165.1.1 — Plant cytotoxins

Domain ID domain_id	d2zr1d1
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	d2zr1d2
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

CATH v4.4 (8 domains)

Domain ID domain_id	2zr1A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	420 — Ricin (A subunit); domain 1
Homologous superfamily homologous superfamily	10 — Ricin (A subunit), domain 1

Domain ID domain_id	2zr1A02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily	10 — Ricin (A Subunit), domain 2

Domain ID domain_id	2zr1B01
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	2zr1B02
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	2zr1C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	420 — Ricin (A subunit); domain 1
Homologous superfamily homologous superfamily	10 — Ricin (A subunit), domain 1

Domain ID domain_id	2zr1C02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily	10 — Ricin (A Subunit), domain 2

Domain ID domain_id	2zr1D01
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	2zr1D02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	137.050 Å
Unit-cell length b length_b	137.050 Å
Unit-cell length c length_c	214.424 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	19.880 Å
R factor r_factor	0.1990
R_work r_work	0.1990
R_free r_free	0.2270

Agglutinin from Abrus Precatorius

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

Agglutinin-1 chain A

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

2zr1__assembly_1__model_1

2zr1__assembly_1__model_1 | I(q)

2zr1__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (5)

Agglutinin from Abrus Precatorius

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

Agglutinin-1 chain A

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

2zr1__assembly_1__model_1

2zr1__assembly_1__model_1 | I(q)

2zr1__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (5)