2ag2

Crystal Structure Analysis of GM2-activator protein complexed with Phosphatidylcholine

Method: X-RAY DIFFRACTION

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

Ganglioside GM2 activator

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 2 ISOPROPYL ALCOHOL × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 1 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 ISOPROPYL ALCOHOL × 3 2-(((R)-2,3-DIHYDROXYPROPYL)PHOSPHORYLOXY)-N,N,N-TRIMETHYLETHANAMINIUM × 1 OLEIC ACID × 1 MYRISTIC ACID × 1 LAURIC ACID × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE × 1 ISOPROPYL ALCOHOL × 5 2-(((R)-2,3-DIHYDROXYPROPYL)PHOSPHORYLOXY)-N,N,N-TRIMETHYLETHANAMINIUM × 1 OLEIC ACID × 1 MYRISTIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SAP3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–164； UniProt 32–193 Author chain B； PDBConstruct 3–164； UniProt 32–193 Author chain C； PDBConstruct 3–164； UniProt 32–193

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	2ag2
Deposition date deposition_date	2005-07-26
Structure title title	Crystal Structure Analysis of GM2-activator protein complexed with Phosphatidylcholine
Keywords keywords	phospholipid-protein complex, lipid acyl chain stacking, packaging, LIPID BINDING PROTEIN; LIPID 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.

2ag2__assembly_2__model_1

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

Download this curve (.dat)

2ag2__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ag2__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	17.46 Å
Rg (electron density)	15.86 Å
Total Rg	16.94 Å
Atom count	1356
Residues	164
Excluded volume	25040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ag2__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ag2__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2ag2__assembly_3__model_1`	monomeric （1）	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 (10)

Entity 1 Entity 1 polymer

Description description	Ganglioside GM2 activator
Molecular weight formula_weight	17827.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4639

HMSSFSWDNCDEGKDPAVIRSLTLEPDPIVVPGNVTLSVVGSTSVPLSSPLKVDLVLEKEVAGLWIKIPCTDYIGSCTFEHFCDVLDMLIPTGEPCPEPLRTYGLPCHCPFKEGTYSLPKSEFVVPDLELPSWLTTGNYRIESVLSSSGKRLGCIKIAASLKGI

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 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	(7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE
Molecular weight formula_weight	524.7 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 6 Entity 6 non-polymer

Description description	2-(((R)-2,3-DIHYDROXYPROPYL)PHOSPHORYLOXY)-N,N,N-TRIMETHYLETHANAMINIUM
Molecular weight formula_weight	258.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	OLEIC ACID
Molecular weight formula_weight	282.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	MYRISTIC ACID
Molecular weight formula_weight	228.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	LAURIC ACID
Molecular weight formula_weight	200.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	594

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d2ag2a2
Class class	b — All beta proteins
Fold Fold fold	b.95 — Ganglioside M2 (gm2) activator
Superfamily Superfamily superfamily	b.95.1 — Ganglioside M2 (gm2) activator
Family Family family	b.95.1.1 — Ganglioside M2 (gm2) activator

Domain ID domain_id	d2ag2a3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2ag2b2
Class class	b — All beta proteins
Fold Fold fold	b.95 — Ganglioside M2 (gm2) activator
Superfamily Superfamily superfamily	b.95.1 — Ganglioside M2 (gm2) activator
Family Family family	b.95.1.1 — Ganglioside M2 (gm2) activator

Domain ID domain_id	d2ag2b3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2ag2c_
Class class	b — All beta proteins
Fold Fold fold	b.95 — Ganglioside M2 (gm2) activator
Superfamily Superfamily superfamily	b.95.1 — Ganglioside M2 (gm2) activator
Family Family family	b.95.1.1 — Ganglioside M2 (gm2) activator

CATH v4.4 (3 domains)

Domain ID domain_id	2ag2A00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	220 — Ganglioside M2 Activator Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Ganglioside GM2 activator

Domain ID domain_id	2ag2B00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	220 — Ganglioside M2 Activator Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Ganglioside GM2 activator

Domain ID domain_id	2ag2C00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	220 — Ganglioside M2 Activator Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Ganglioside GM2 activator

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Unit-cell length a length_a	63.530 Å
Unit-cell length b length_b	86.190 Å
Unit-cell length c length_c	120.480 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	19.760 Å
R factor r_factor	0.1880
R_work r_work	0.1880
R_free r_free	0.2310

Crystal Structure Analysis of GM2-activator protein complexed with Phosphatidylcholine

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

Ganglioside GM2 activator

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

2ag2__assembly_2__model_1

2ag2__assembly_2__model_1 | I(q)

2ag2__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (5 domains)

CATH v4.4 (3 domains)

7. Citations (4)

Crystal Structure Analysis of GM2-activator protein complexed with Phosphatidylcholine

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

Ganglioside GM2 activator

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

2ag2__assembly_2__model_1

2ag2__assembly_2__model_1 | I(q)

2ag2__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (5 domains)

CATH v4.4 (3 domains)

7. Citations (4)