SAXSdb — 3nfk

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

Tyrosine-protein phosphatase non-receptor type 4

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Glycoprotein G × 1 （P03524） GLYCEROL × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Glycoprotein G × 1 （P03524） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Glycoprotein G × 2 （P03524） GLYCEROL × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PTN4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–107； UniProt 499–604 Author chain B； PDBConstruct 2–107； UniProt 499–604

Glycoprotein G

OrganismNot specified

UniProt P03524

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Tyrosine-protein phosphatase non-receptor type 4 × 1 （P29074） GLYCEROL × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Tyrosine-protein phosphatase non-receptor type 4 × 1 （P29074） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Tyrosine-protein phosphatase non-receptor type 4 × 2 （P29074） GLYCEROL × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VGLG_RABVE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–13； UniProt 512–524 Author chain D； PDBConstruct 1–13； UniProt 512–524

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	3nfk
Deposition date deposition_date	2010-06-10
Structure title title	Crystal structure of the PTPN4 PDZ domain complexed with the C-terminus of a rabies virus G protein
Keywords keywords	PDZ-PDZ-binding site complex, PROTEIN BINDING; 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.

3nfk__assembly_1__model_1

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

Download this curve (.dat)

3nfk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3nfk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.25 Å
Rg (electron density)	12.67 Å
Total Rg	14.08 Å
Atom count	826
Residues	105
Excluded volume	14638 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3nfk__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3nfk__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3nfk__assembly_3__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	Tyrosine-protein phosphatase non-receptor type 4
Molecular weight formula_weight	11694.4 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	1761

GSSPEKPTPNGGIPHDNLVLIRMKPDENGRFGFNVKGGYDQKMPVIVSRVAPGTPADLCVPRLNEGDQVVLINGRDIAEHTHDQVVLFIKASCERHSGELMLLVRPN

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	Glycoprotein G
Molecular weight formula_weight	1476.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

SWESHKSGGETRL

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	181

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3nfka_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.1 — PDZ domain

Domain ID domain_id	d3nfkb_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.1 — PDZ domain

CATH v4.4 (2 domains)

Domain ID domain_id	3nfkA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3nfkB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

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Unit-cell length a length_a	53.430 Å
Unit-cell length b length_b	53.700 Å
Unit-cell length c length_c	81.800 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.430 Å
Low-resolution limit resolution_low	14.410 Å
R factor r_factor	0.1927
R_work r_work	0.1921
R_free r_free	0.2039

Crystal structure of the PTPN4 PDZ domain complexed with the C-terminus of a rabies virus G protein

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

Tyrosine-protein phosphatase non-receptor type 4

State in the Current Structure

Other States of the Same Protein in the Database

Glycoprotein G

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

3nfk__assembly_1__model_1

3nfk__assembly_1__model_1 | I(q)

3nfk__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the PTPN4 PDZ domain complexed with the C-terminus of a rabies virus G protein

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

Tyrosine-protein phosphatase non-receptor type 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Glycoprotein G

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

3nfk__assembly_1__model_1

3nfk__assembly_1__model_1 | I(q)

3nfk__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)