SAXSdb — 1abr

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

ABRIN-A

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 262–528	Not recorded	ABRIN-A × 1 ;beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-L-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose ; × 1 ;beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose ; × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.14 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	ABRA_ABRPR
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–267； UniProt 262–528

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	1abr
Deposition date deposition_date	1994-11-11
Structure title title	CRYSTAL STRUCTURE OF ABRIN-A
Keywords keywords	;GLYCOSIDASE-CARBOHYDRATE complex, LECTIN, LECTIN (AGGLUTININ), GLYCOPROTEIN, PLANT SEED PROTEIN, PLANT TOXIN, PROTEIN SYNTHESIS INHIBITOR, TOXIN ;; GLYCOSIDASE/CARBOHYDRATE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	26.15 Å
Radius of gyration Rg (electron density) rg_electron	25.13 Å
Forward intensity I(0) i0	62640100.00
Molecular weight molecular_weight	59970.0 kDa
Excluded volume excluded_volume	74290 Å³
Envelope volume envelope_volume	88267 Å³
Hydration-shell volume shell_volume	29505 Å³
Envelope diameter envelope_diameter	85.8 Å
Shell Rg shell_rg	32.24 Å
Envelope Rg envelope_rg	25.09 Å
Shape Rg shape_rg	25.13 Å
Total Rg total_rg	25.85 Å
Total atoms total_atoms	5198
Residues n_residues	518
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	83.1 Å
Rg (real space) rg_real	26.13 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	6.2640e+07
I(0) uncertainty (real space) i0_real_error	9.2610e+05
Rg (reciprocal space) rg_reciprocal	26.14 Å
I(0) (reciprocal space) i0_reciprocal	62640000.0000
Solution quality estimate total_estimate	0.9006
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.6 Å
Skewness Skewness skewness	0.329
Kurtosis Kurtosis kurtosis	-0.417
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12510000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.954

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	ABRIN-A
Molecular weight formula_weight	28124.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5798

EDRPIKFSTEGATSQSYKQFIEALRERLRGGLIHDIPVLPDPTTLQERNRYITVELSNSDTESIEVGIDVTNAYVVAYRAGTQSYFLRDAPSSASDYLFTGTDQHSLPFYGTYGDLERWAHQSRQQIPLGLQALTHGISFFRSGGNDNEEKARTLIVIIQMVAEAARFRYISNRVRVSIQTGTAFQPDAAMISLENNWDNLSRGVQESVQDTFPNQVTLTNIRNEPVIVDSLSHPTVAVLALMLFVCNPPN

来源 Source

来源生物 organism	Abrus precatorius
通用名 common_name	Indian licorice
NCBI Class编号 ncbi_taxonomy_id	3816

Entity 2 Entity 2 polymer

Description description	ABRIN-A
Molecular weight formula_weight	30111.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

IVEKSKICSSRYEPTVRIGGRDGMCVDVYDNGYHNGNRIIMWKCKDRLEENQLWTLKSDKTIRSNGKCLTTYGYAPGSYVMIYDCTSAVAEATYWEIWDNGTIINPKSALVLSAESSSMGGTLTVQTNEYLMRQGWRTGNNTSPFVTSISGYSDLCMQAQGSNVWMADCDSNKKEQQWALYTDGSIRSVQNTNNCLTSKDHKQGSTILLMGCSNGWASQRWVFKNDGSIYSLYDDMVMDVKGSDPSLKQIILWPYTGKPNQIWLTLF

Entity 3 Entity 3 branched

Description description	;beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-L-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose ;
Molecular weight formula_weight	910.8 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 branched

Description description	;beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose ;
Molecular weight formula_weight	910.8 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	200

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1abra_
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	d1abrb1
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	d1abrb2
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 (4 domains)

Domain ID domain_id	1abrA01
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	1abrA02
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	1abrB01
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	1abrB02
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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8. Citations (4)

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Unit-cell length a length_a	84.580 Å
Unit-cell length b length_b	73.070 Å
Unit-cell length c length_c	48.230 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.20 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.140 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1890
R_work r_work	0.1890
R_free r_free	—

fit	/app/data/saxs_computation/ab/1abr/1abr.fit
pddf	/app/data/pr_computation/ab/1abr/1abr.pr.out
profile	/app/data/saxs_computation/ab/1abr/1abr.dat

CRYSTAL STRUCTURE OF ABRIN-A

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

ABRIN-A

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

8. Citations (4)

9. Files and Curves (10)

Files (7)

Curves (3)