SAXSdb — 2q46

▼

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

Protein At5g02240

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y5224_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–253； UniProt 2–253 Author chain B； PDBConstruct 2–253； UniProt 2–253

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2q46
Deposition date deposition_date	2007-05-31
Structure title title	Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g02240
Keywords keywords	;Ensemble Refinement, Refinement Methodology Development, AT5G02240, NADP, Structural Genomics, Protein Structure Initiative, PSI, Center for Eukaryotic Structural Genomics, CESG, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2q46__assembly_1__model_5

Assembly 1 · Model 5 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2q46__assembly_1__model_5 | I(q)

100 plotted points; both axes use logarithmic scales.

2q46__assembly_1__model_5 | P(r) · Pending

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

Rg（Guinier）	18.93 Å
Rg (electron density)	17.84 Å
Total Rg	18.81 Å
Atom count	1956
Residues	253
Excluded volume	34783 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2q46__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`2q46__assembly_1__model_2`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`2q46__assembly_1__model_3`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`2q46__assembly_1__model_4`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	5	`2q46__assembly_1__model_5`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	6	`2q46__assembly_1__model_6`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	7	`2q46__assembly_1__model_7`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	8	`2q46__assembly_1__model_8`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2q46__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	2	`2q46__assembly_2__model_2`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	3	`2q46__assembly_2__model_3`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	4	`2q46__assembly_2__model_4`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	5	`2q46__assembly_2__model_5`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	6	`2q46__assembly_2__model_6`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	7	`2q46__assembly_2__model_7`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	8	`2q46__assembly_2__model_8`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Protein At5g02240
Molecular weight formula_weight	27092.8 kDa
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	34496

SANLPTVLVTGASGRTGQIVYKKLKEGSDKFVAKGLVRSAQGKEKIGGEADVFIGDITDADSINPAFQGIDALVILTSAVPKMKPGFDPTKGGRPEFIFEDGQYPEQVDWIGQKNQIDAAKVAGVKHIVVVGSMGGTNPDHPLNKLGNGNILVWKRKAEQYLADSGTPYTIIRAGGLLDKEGGVRELLVGKDDELLQTDTKTVPRADVAEVCIQALLFEEAKNKAFDLGSKPEGTSTPTKDFKALFSQVTSRF

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

Entity 2 Entity 2 non-polymer

Description description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	743.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	400

▼

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2q46a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

Domain ID domain_id	d2q46a3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2q46b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

Domain ID domain_id	d2q46b3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	2q46A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2q46B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

▶

Unit-cell length a length_a	46.750 Å
Unit-cell length b length_b	69.799 Å
Unit-cell length c length_c	83.828 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.01 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	23.565 Å
R factor r_factor	0.2090
R_work r_work	0.2090
R_free r_free	0.2670

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g02240

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

Protein At5g02240

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

2q46__assembly_1__model_5

2q46__assembly_1__model_5 | I(q)

2q46__assembly_1__model_5 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g02240

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

Protein At5g02240

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

2q46__assembly_1__model_5

2q46__assembly_1__model_5 | I(q)

2q46__assembly_1__model_5 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)