SAXSdb — 5mxw

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

Class 10 plant pathogenesis-related protein

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	UNKNOWN LIGAND × 16 SODIUM ION × 1 N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide × 1 (2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol × 1 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 1–156； UniProt 2–157

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	5mxw
Deposition date deposition_date	2017-01-25
Structure title title	Crystal structure of yellow lupin LLPR-10.2B protein in complex with melatonin and trans-zeatin.
Keywords keywords	plant protein, phytohormon binding protein, PR-10 protein, melatonin; 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.

5mxw__assembly_1__model_1

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

Download this curve (.dat)

5mxw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5mxw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.60 Å
Rg (electron density)	15.29 Å
Total Rg	16.49 Å
Atom count	1212
Residues	155
Excluded volume	21619 Å³
Maximum q	0.500 Å⁻¹

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

Entity 1 Entity 1 polymer

Description description	Class 10 plant pathogenesis-related protein
Molecular weight formula_weight	16660.7 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	1391

GVFTFQDEYTSTIAPAKLYKALVTDADIIIPKAVETIQSVEIVEGNGGPGTIKKLTFIEGGESKYVLHKIEAIDEANLGYNYSIVGGVGLPDTIEKISFETKLVEGANGGSIGKVTIKIETKGDAQPNEEEGKAAKARGDAFFKAIESYLSAHPDY

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	UNKNOWN LIGAND
Source method src_method	syn
Copy count entity_count	16

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	1

Entity 4 Entity 4 non-polymer

Description description	N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide
Molecular weight formula_weight	232.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	(2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol
Molecular weight formula_weight	219.2 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	148

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5mxwa_
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	5mxwA00
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 (11)

;PR-10 proteins as potential mediators of melatonin-cytokinin cross-talk in plants: crystallographic studies of LlPR-10.2B isoform from yellow lupine. ;

FEBS J. (2018)

PMID: 29630775 · DOI: 10.1111/febs.14455 PRIMARY

Crystal Structure of Hyp-1, a Hypericum perforatum PR-10 Protein, in Complex with Melatonin.

Front Plant Sci (2016)

PMID: 27242869 · DOI: 10.3389/fpls.2016.00668

Crystallographic and CD probing of ligand-induced conformational changes in a plant PR-10 protein.

J. Struct. Biol. (2016)

PMID: 26644353 · DOI: 10.1016/j.jsb.2015.11.008

;ANS complex of St John's wort PR-10 protein with 28 copies in the asymmetric unit: a fiendish combination of pseudosymmetry with tetartohedral twinning. ;

Acta Crystallogr. D Biol. Crystallogr. (2015)

PMID: 25849394 · DOI: 10.1107/S1399004715001388

;Specific binding of gibberellic acid by cytokinin-specific binding proteins: a new aspect of plant hormone-binding proteins with the PR-10 fold. ;

Acta Crystallogr. D Biol. Crystallogr. (2014)

PMID: 25004979 · DOI: 10.1107/S1399004714010578

The landscape of cytokinin binding by a plant nodulin.

Acta Crystallogr. D Biol. Crystallogr. (2013)

PMID: 24311578 · DOI: 10.1107/S0907444913021975

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

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. D Biol. Crystallogr. (2005)

PMID: 15608381 · DOI: 10.1107/S0907444904028173

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

Unit-cell length a length_a	74.400 Å
Unit-cell length b length_b	74.400 Å
Unit-cell length c length_c	67.310 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	1.570 Å
Low-resolution limit resolution_low	46.590 Å
R factor r_factor	0.1858
R_work r_work	0.1850
R_free r_free	0.2059

Crystal structure of yellow lupin LLPR-10.2B protein in complex with melatonin and trans-zeatin.

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

Class 10 plant pathogenesis-related protein

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

5mxw__assembly_1__model_1

5mxw__assembly_1__model_1 | I(q)

5mxw__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 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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (11)

Crystal structure of yellow lupin LLPR-10.2B protein in complex with melatonin and trans-zeatin.

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

Class 10 plant pathogenesis-related protein

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

5mxw__assembly_1__model_1

5mxw__assembly_1__model_1 | I(q)

5mxw__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 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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (11)