SAXSdb — 2pyw

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

Uncharacterized protein

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 2 MAGNESIUM ION × 5 5-S-methyl-5-thio-alpha-D-ribofuranose × 2 ADENOSINE-5'-DIPHOSPHATE × 2 1,2-ETHANEDIOL × 5 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9C6D2_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–420； UniProt 1–420 Author chain B； PDBConstruct 1–420； UniProt 1–420

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	2pyw
Deposition date deposition_date	2007-05-16
Structure title title	Structure of A. thaliana 5-methylthioribose kinase in complex with ADP and MTR
Keywords keywords	5-methylthioribose kinase, plant methionine recycling, refolding, Transferase; TRANSFERASE
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.

2pyw__assembly_1__model_1

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

Download this curve (.dat)

2pyw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2pyw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.12 Å
Rg (electron density)	29.41 Å
Total Rg	30.03 Å
Atom count	6753
Residues	828
Excluded volume	120150 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2pyw__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Description description	Uncharacterized protein
Molecular weight formula_weight	48130.7 kDa
EC 编号 ec_number	2.7.1.100
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7531

MSFEEFTPLNEKSLVDYIKSTPALSSKIGADKSDDDLVIKEVGDGNLNFVFIVVGSSGSLVIKQALPYIRCIGESWPMTKERAYFEATTLRKHGNLSPDHVPEVYHFDRTMALIGMRYLEPPHIILRKGLIAGIEYPFLADHMSDYMAKTLFFTSLLYHDTTEHRRAVTEFCGNVELCRLTEQVVFSDPYRVSTFNRWTSPYLDDDAKAVREDSALKLEIAELKSMFCERAQALIHGDLHTGSVMVTQDSTQVIDPEFSFYGPMGFDIGAYLGNLILAFFAQDGHATQENDRKEYKQWILRTIEQTWNLFNKRFIALWDQNKDGPGEAYLADIYNNTEVLKFVQENYMRNLLHDSLGFGAAKMIRRIVGVAHVEDFESIEEDKRRAICERSALEFAKMLLKERRKFKSIGEVVSAIQQQS

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	thale cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

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

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	5

Entity 4 Entity 4 non-polymer

Description description	5-S-methyl-5-thio-alpha-D-ribofuranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	778

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2pywa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

Domain ID domain_id	d2pywb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	2pywA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	2pywA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1200 — Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Aminoglycoside phosphotransferase (APH), C-terminal lobe

Domain ID domain_id	2pywB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	2pywB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1200 — Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Aminoglycoside phosphotransferase (APH), C-terminal lobe

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Unit-cell length a length_a	162.460 Å
Unit-cell length b length_b	82.240 Å
Unit-cell length c length_c	91.080 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	117.83 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	80.580 Å
R factor r_factor	0.1648
R_work r_work	0.1630
R_free r_free	0.1972

Structure of A. thaliana 5-methylthioribose kinase in complex with ADP and MTR

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

Uncharacterized 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

2pyw__assembly_1__model_1

2pyw__assembly_1__model_1 | I(q)

2pyw__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of A. thaliana 5-methylthioribose kinase in complex with ADP and MTR

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

Uncharacterized 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

2pyw__assembly_1__model_1

2pyw__assembly_1__model_1 | I(q)

2pyw__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)