SAXSdb — 3np5

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

Receptor-type tyrosine-protein phosphatase-like N

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	CALCIUM ION × 2 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PTPRN_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–89； UniProt 470–558 Author chain B； PDBConstruct 1–89； UniProt 470–558 Author chain C； PDBConstruct 1–89； UniProt 470–558 Author chain D； PDBConstruct 1–89； UniProt 470–558

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	3np5
Deposition date deposition_date	2010-06-27
Structure title title	Crystal structure of an abridged form of the mature ectodomain of the human receptor-type protein tyrosine phosphatase ICA512/IA-2 AT pH 4.5
Keywords keywords	;IA-2, ICA-512, PROTEIN-TYROSINE PHOSPHATASE, TRANSMEMBRANE PROTEIN, DIABETES, AUTOIMMUNITY, PROTEOLYSIS, GLYCOPROTEIN, RECEPTOR, HYDROLASE ;; HYDROLASE
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.

3np5__assembly_2__model_1

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

Download this curve (.dat)

3np5__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3np5__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	17.47 Å
Rg (electron density)	16.10 Å
Total Rg	17.12 Å
Atom count	1326
Residues	175
Excluded volume	23757 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3np5__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3np5__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3np5__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Description description	Receptor-type tyrosine-protein phosphatase-like N
Molecular weight formula_weight	9637.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	2874

EYGYIVTDQKPLSLAAGVKLLEILAEHVHMSSGSFINISVVGPALTFRIRHNEQNLSLADVTQQAGLVKSELEAQTGLQILQTGVGQRE

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 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 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	132

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3np5A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2470 — Protein-tyrosine phosphatase receptor IA-2 ectodomain

Domain ID domain_id	3np5B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2470 — Protein-tyrosine phosphatase receptor IA-2 ectodomain

Domain ID domain_id	3np5C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2470 — Protein-tyrosine phosphatase receptor IA-2 ectodomain

Domain ID domain_id	3np5D00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2470 — Protein-tyrosine phosphatase receptor IA-2 ectodomain

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Unit-cell length a length_a	44.662 Å
Unit-cell length b length_b	44.662 Å
Unit-cell length c length_c	168.665 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	16

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	19.840 Å
R factor r_factor	—
R_work r_work	0.1611
R_free r_free	0.2385

Crystal structure of an abridged form of the mature ectodomain of the human receptor-type protein tyrosine phosphatase ICA512/IA-2 AT pH 4.5

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

Receptor-type tyrosine-protein phosphatase-like N

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

3np5__assembly_2__model_1

3np5__assembly_2__model_1 | I(q)

3np5__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 (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) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)

Crystal structure of an abridged form of the mature ectodomain of the human receptor-type protein tyrosine phosphatase ICA512/IA-2 AT pH 4.5

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

Receptor-type tyrosine-protein phosphatase-like N

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

3np5__assembly_2__model_1

3np5__assembly_2__model_1 | I(q)

3np5__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 (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) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)