SAXSdb — 1py1

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

ADP-ribosylation factor binding protein GGA1

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	Beta-secretase × 2 （P56817） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Beta-secretase × 2 （P56817） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GGA1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–158； UniProt 2–157 Author chain B； PDBConstruct 2–158； UniProt 2–157 Author chain C； PDBConstruct 2–158； UniProt 2–157 Author chain D； PDBConstruct 2–158； UniProt 2–157

Beta-secretase

OrganismNot specified

UniProt P56817

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	ADP-ribosylation factor binding protein GGA1 × 2 （Q9UJY5） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	ADP-ribosylation factor binding protein GGA1 × 2 （Q9UJY5） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BACE1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–8； UniProt 494–501 Author chain F； PDBConstruct 1–8； UniProt 494–501 Author chain G； PDBConstruct 1–8； UniProt 494–501 Author chain H； PDBConstruct 1–8； UniProt 494–501

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	1py1
Deposition date deposition_date	2003-07-07
Structure title title	Complex of GGA1-VHS domain and beta-secretase C-terminal phosphopeptide
Keywords keywords	VHS DOMAIN OF GGA1, BETA-SECRETASE, PROTEIN-PEPTIDE COMPLEX, SUPER HELIX, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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.

1py1__assembly_1__model_1

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

Download this curve (.dat)

1py1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1py1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.57 Å
Rg (electron density)	19.51 Å
Total Rg	20.42 Å
Atom count	2377
Residues	293
Excluded volume	42740 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1py1__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1py1__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	ADP-ribosylation factor binding protein GGA1
Molecular weight formula_weight	17958.6 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	4776

GSEPAMEPETLEARINRATNPLNKELDWASINGFCEQLNEDFEGPPLATRLLAHKIQSPQEWEAIQALTVLETCMKSCGKRFHDEVGKFRFLNELIKVVSPKYLGSRTSEKVKNKILELLYSWTVGLPEEVKIAEAYQMLKKQGIVKSDPKLPDDTTF

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Beta-secretase
Molecular weight formula_weight	955.0 kDa
EC 编号 ec_number	3.4.23.-
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

ADDISLLK

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	37

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1py1a_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.9 — ENTH/VHS domain
Family Family family	a.118.9.2 — VHS domain

Domain ID domain_id	d1py1b_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.9 — ENTH/VHS domain
Family Family family	a.118.9.2 — VHS domain

Domain ID domain_id	d1py1c_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.9 — ENTH/VHS domain
Family Family family	a.118.9.2 — VHS domain

Domain ID domain_id	d1py1d_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.9 — ENTH/VHS domain
Family Family family	a.118.9.2 — VHS domain

CATH v4.4 (4 domains)

Domain ID domain_id	1py1A00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	1py1B00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	1py1C00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	1py1D00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	90 —

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Unit-cell length a length_a	70.140 Å
Unit-cell length b length_b	95.420 Å
Unit-cell length c length_c	107.970 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 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	39.450 Å
R factor r_factor	0.2360
R_work r_work	0.2360
R_free r_free	0.2880

Complex of GGA1-VHS domain and beta-secretase C-terminal phosphopeptide

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

ADP-ribosylation factor binding protein GGA1

State in the Current Structure

Other States of the Same Protein in the Database

Beta-secretase

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

1py1__assembly_1__model_1

1py1__assembly_1__model_1 | I(q)

1py1__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Complex of GGA1-VHS domain and beta-secretase C-terminal phosphopeptide

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

ADP-ribosylation factor binding protein GGA1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Beta-secretase

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

1py1__assembly_1__model_1

1py1__assembly_1__model_1 | I(q)

1py1__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)