SAXSdb — 7ykh

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

Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	SAPAP1 × 1 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	SAPAP1 × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MAGI2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–234； UniProt 9–238 Author chain C； PDBConstruct 5–234； UniProt 9–238

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	7ykh
Deposition date deposition_date	2022-07-22
Structure title title	Crystal structure of MAGI2 PDZ0-GK domain in complex with phospho-SAPAP1 GBR2 peptide
Keywords keywords	MAGI2, PDZ0-GK, SAPAP1, GBR2, phosphorylated peptide, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
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.

7ykh__assembly_2__model_1

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

Download this curve (.dat)

7ykh__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7ykh__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	19.06 Å
Rg (electron density)	18.22 Å
Total Rg	19.07 Å
Atom count	1503
Residues	193
Excluded volume	26704 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7ykh__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7ykh__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2
Molecular weight formula_weight	25982.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	3060

GPGSSHWTSKVHESVIGRNPEGQLGFELKGGAENGQFPYLGEVKPGKVAYESGSKLVSEELLLEVNETPVAGLTIRDVLAVIKHCKDPLRLKCVKQGGIVDKDLRHYLNLRFQKGSVDHELQQIIRDNLYLRTVPCTTRPHKEGEVPGVDYIFITVEEFMELEKSGALLESGTYEDNYYGTPKPPAEPAPLLNVTDQILPGATPSAEGKRKRNKSVTNMEKASIEPPEEEEEER

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	SAPAP1
Molecular weight formula_weight	1702.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

ARRESYLKATQPSL

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli BL21(DE3)

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	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	36

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7ykhA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	63 — Guanylate Kinase phosphate binding domain
Homologous superfamily homologous superfamily	10 — Guanylate Kinase phosphate binding domain

Domain ID domain_id	7ykhC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	63 — Guanylate Kinase phosphate binding domain
Homologous superfamily homologous superfamily	10 — Guanylate Kinase phosphate binding domain

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Unit-cell length a length_a	55.212 Å
Unit-cell length b length_b	61.540 Å
Unit-cell length c length_c	65.104 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.79 °
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	2.500 Å
Low-resolution limit resolution_low	40.609 Å
R factor r_factor	0.2071
R_work r_work	0.2038
R_free r_free	0.2644

Crystal structure of MAGI2 PDZ0-GK domain in complex with phospho-SAPAP1 GBR2 peptide

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

Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2

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

7ykh__assembly_2__model_1

7ykh__assembly_2__model_1 | I(q)

7ykh__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of MAGI2 PDZ0-GK domain in complex with phospho-SAPAP1 GBR2 peptide

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

Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7ykh__assembly_2__model_1

7ykh__assembly_2__model_1 | I(q)

7ykh__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)