SAXSdb — 5k23

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

Protein tyrosine phosphatase type IVA 2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Metal transporter CNNM3 × 2 （Q8NE01）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	Metal transporter CNNM3 × 4 （Q8NE01）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TP4A2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 23–189； UniProt 1–167

Metal transporter CNNM3

Homo sapiens

UniProt Q8NE01

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Protein tyrosine phosphatase type IVA 2 × 2 （Q12974）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	Protein tyrosine phosphatase type IVA 2 × 4 （Q12974）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CNNM3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 12–155； UniProt 309–452

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	5k23
Deposition date deposition_date	2016-05-18
Structure title title	Crystal structure of the complex between human phosphatase PRL-2 in the oxidized state with the Bateman domain of human magnesium transporter CNNM3
Keywords keywords	Complex, phosphatase, magnesium transporter, protein binding, HYDROLASE, HYDROLASE-TRANSPORTER PROTEIN-PROTEIN BINDING complex; HYDROLASE/TRANSPORTER PROTEIN/PROTEIN BINDING
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.

5k23__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5k23__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5k23__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	45.23 Å
Rg (electron density)	44.58 Å
Total Rg	44.60 Å
Atom count	9604
Residues	1220
Excluded volume	171710 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5k23__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5k23__assembly_2__model_1`	octameric （8）	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 (2)

Entity 1 Entity 1 polymer

Description description	Protein tyrosine phosphatase type IVA 2
Molecular weight formula_weight	21856.3 kDa
EC 编号 ec_number	3.1.3.48
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	2401

MSYYHHHHHHLESTSLYKKAGFMNRPAPVEISYENMRFLITHNPTNATLNKFTEELKKYGVTTLVRVCDATYDKAPVEKEGIHVLDWPFDDGAPPPNQIVDDWLNLLKTKFREEPGCCVAVHCVAGLGRAPVLVALALIECGMKYEDAVQFIRQKRRGAFNSKQLLYLEKYRPKMRLRFRDTNGHCCVQ

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Metal transporter CNNM3
Molecular weight formula_weight	17634.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GPLNMIQGVLELRCRTVEDVLTPLEDCFMLDASTVLDFGVLASIMQSGHTRIPVYEEERSNIVDMLYLKDLAFVDPEDCTPLSTITRFYNHPLHFVFNDTKLDAVLEEFKRGKSHLAIVQKVNNEGEGDPFYEVLGLVTLEDVIEEIIRSEILDE

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5k23a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.45 — (Phosphotyrosine protein) phosphatases II
Superfamily Superfamily superfamily	c.45.1 — (Phosphotyrosine protein) phosphatases II
Family Family family	c.45.1.1 — Dual specificity phosphatase-like

CATH v4.4 (2 domains)

Domain ID domain_id	5k23A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily	10 — Protein tyrosine phosphatase superfamily

Domain ID domain_id	5k23C00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	580 — CBS-domain
Homologous superfamily homologous superfamily	10 — CBS-domain

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Unit-cell length a length_a	51.156 Å
Unit-cell length b length_b	124.490 Å
Unit-cell length c length_c	159.048 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.960 Å
Low-resolution limit resolution_low	49.020 Å
R factor r_factor	0.2079
R_work r_work	0.2050
R_free r_free	0.2636

Crystal structure of the complex between human phosphatase PRL-2 in the oxidized state with the Bateman domain of human magnesium transporter CNNM3

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

Protein tyrosine phosphatase type IVA 2

State in the Current Structure

Other States of the Same Protein in the Database

Metal transporter CNNM3

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

5k23__assembly_2__model_1

5k23__assembly_2__model_1 | I(q)

5k23__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the complex between human phosphatase PRL-2 in the oxidized state with the Bateman domain of human magnesium transporter CNNM3

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

Protein tyrosine phosphatase type IVA 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Metal transporter CNNM3

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

5k23__assembly_2__model_1

5k23__assembly_2__model_1 | I(q)

5k23__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)