SAXSdb — 3e85

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

PR10.2B

Lupinus luteus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	1,3-DIPHENYLUREA × 4 SODIUM ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9LLQ2_LUPLU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–158； UniProt 1–158

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	3e85
Deposition date deposition_date	2008-08-19
Structure title title	Crystal Structure of Pathogenesis-related Protein LlPR-10.2B from yellow lupine in complex with Diphenylurea
Keywords keywords	;PLANT HORMONES, CYTOKININ, DIPHENYLUREA, PLANT PR-10 PROTEIN, YELLOW LUPINE, Pathogenesis-related protein, Plant defense, 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.

3e85__assembly_1__model_1

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

Download this curve (.dat)

3e85__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3e85__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.48 Å
Rg (electron density)	14.93 Å
Total Rg	16.26 Å
Atom count	1221
Residues	154
Excluded volume	21979 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3e85__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	PR10.2B
Molecular weight formula_weight	16906.0 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	1369

MGVFTFQDEYTSTIAPAKLYKALVTDADIIIPKAVETIQSVEIVEGNGGPGTIKKLTFIEGGESKYVLHKIEAIDEANLGYNYSIVGGVGLPDTIEKISFETKLVEGANGGSIGKVTIKIETKGDAQPNEEEGKAAKARGDAFFKAIESYLSAHPDYN

Source Source

Source organism organism	Lupinus luteus
Common name common_name	European yellow lupin
NCBI taxonomy ID ncbi_taxonomy_id	3873
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,3-DIPHENYLUREA
Molecular weight formula_weight	212.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
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	134

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3e85a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.3 — Bet v1-like
Family Family family	d.129.3.1 — Pathogenesis-related protein 10 (PR10)-like

CATH v4.4 (1 domains)

Domain ID domain_id	3e85A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	530 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4
Homologous superfamily homologous superfamily	20 — START domain

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7. Citations (7)

Cytokinin-induced structural adaptability of a Lupinus luteus PR-10 protein.

Febs J. (2009)

PMID: 19220853 · DOI: 10.1111/j.1742-4658.2009.06892.x PRIMARY

Lupinus luteus Pathogenesis-Related Protein as a Reservoir for Cytokinin

J.Mol.Biol. (2008)

PMID: 18406424 · DOI: 10.1016/j.jmb.2008.03.027

Crystal structure of Vigna radiata cytokinin-specific binding protein in complex with zeatin

Plant Cell (2006)

PMID: 16998071 · DOI: 10.1105/tpc.105.037119

Structure of a yellow lupin pathogenesis-related PR-10 protein belonging to a novel subclass

Acta Crystallogr.,Sect.D (2005)

PMID: 15608381 · DOI: 10.1107/S0907444904028173

;Crystal structure of a hypoallergenic isoform of the major birch pollen allergen Bet v 1 and its likely biological function as a plant steroid carrier ;

J.Mol.Biol. (2003)

PMID: 12473456 · DOI: 10.1016/S0022-2836(02)01197-X

Crystal structures of two homologous pathogenesis-related proteins from yellow lupine

J.Mol.Biol. (2002)

PMID: 12079359 · DOI: 10.1016/S0022-2836(02)00385-6

X-ray and NMR structure of Bet v 1, the origin of birch pollen allergy

Nat.Struct.Mol.Biol. (1996)

PMID: 8946858

Unit-cell length a length_a	34.362 Å
Unit-cell length b length_b	73.256 Å
Unit-cell length c length_c	99.956 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.1932
R_work r_work	0.1879
R_free r_free	0.2465

Crystal Structure of Pathogenesis-related Protein LlPR-10.2B from yellow lupine in complex with Diphenylurea

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

PR10.2B

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

3e85__assembly_1__model_1

3e85__assembly_1__model_1 | I(q)

3e85__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

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (7)

Crystal Structure of Pathogenesis-related Protein LlPR-10.2B from yellow lupine in complex with Diphenylurea

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

PR10.2B

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

3e85__assembly_1__model_1

3e85__assembly_1__model_1 | I(q)

3e85__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

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (7)