SAXSdb — 3fro

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

GlgA glycogen synthase

Pyrococcus abyssi

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 PHOSPHATE ION × 3 1,5-anhydro-D-fructose × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9V2J8_PYRAB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–439； UniProt 1–437 Author chain B； PDBConstruct 3–439； UniProt 1–437 Author chain C； PDBConstruct 3–439； UniProt 1–437

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	3fro
Deposition date deposition_date	2009-01-08
Structure title title	Crystal structure of Pyrococcus abyssi glycogen synthase with open and closed conformations
Keywords keywords	GLYCOSYLTRANSFERASE FAMILY, UDP/ADP-GLUCOSE-GLYCOGEN SYNTHASE, TWO ROSSMAN FOLDS, TRANSFERASE; TRANSFERASE
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.

3fro__assembly_1__model_1

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

Download this curve (.dat)

3fro__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fro__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.10 Å
Rg (electron density)	40.59 Å
Total Rg	41.02 Å
Atom count	10502
Residues	1317
Excluded volume	188470 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fro__assembly_1__model_1`	trimeric （3）	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 (5)

Entity 1 Entity 1 polymer

Description description	GlgA glycogen synthase
Molecular weight formula_weight	49341.6 kDa
EC 编号 ec_number	2.4.1.21
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	10635

RHMKVLLLGFEFLPVKVGGLAEALTAISEALASLGHEVLVFTPSHGRFQGEEIGKIRVFGEEVQVKVSYEERGNLRIYRIGGGLLDSEDVYGPGWDGLIRKAVTFGRASVLLLNDLLREEPLPDVVHFHDWHTVFAGALIKKYFKIPAVFTIHRLNKSKLPAFYFHEAGLSELAPYPDIDPEHTGGYIADIVTTVSRGYLIDEWGFFRNFEGKITYVFNGIDCSFWNESYLTGSRDERKKSLLSKFGMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHGNVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIITNETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFSWEKSAERYVKAYTGSIDRAFDFIL

Source Source

Source organism organism	Pyrococcus abyssi
NCBI taxonomy ID ncbi_taxonomy_id	29292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	1,5-anhydro-D-fructose
Molecular weight formula_weight	162.1 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	95

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3froa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.87 — UDP-Glycosyltransferase/glycogen phosphorylase
Superfamily Superfamily superfamily	c.87.1 — UDP-Glycosyltransferase/glycogen phosphorylase
Family Family family	c.87.1.8 — Glycosyl transferases group 1

Domain ID domain_id	d3froa2
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	d3frob1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.87 — UDP-Glycosyltransferase/glycogen phosphorylase
Superfamily Superfamily superfamily	c.87.1 — UDP-Glycosyltransferase/glycogen phosphorylase
Family Family family	c.87.1.8 — Glycosyl transferases group 1

Domain ID domain_id	d3frob2
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	d3froc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.87 — UDP-Glycosyltransferase/glycogen phosphorylase
Superfamily Superfamily superfamily	c.87.1 — UDP-Glycosyltransferase/glycogen phosphorylase
Family Family family	c.87.1.8 — Glycosyl transferases group 1

Domain ID domain_id	d3froc2
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

CATH v4.4 (6 domains)

Domain ID domain_id	3froA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

Domain ID domain_id	3froA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

Domain ID domain_id	3froB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

Domain ID domain_id	3froB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

Domain ID domain_id	3froC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

Domain ID domain_id	3froC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

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Unit-cell length a length_a	74.998 Å
Unit-cell length b length_b	139.913 Å
Unit-cell length c length_c	159.414 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	2.500 Å
Low-resolution limit resolution_low	24.910 Å
R factor r_factor	0.2160
R_work r_work	0.2140
R_free r_free	0.2550

Crystal structure of Pyrococcus abyssi glycogen synthase with open and closed conformations

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

GlgA glycogen synthase

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

3fro__assembly_1__model_1

3fro__assembly_1__model_1 | I(q)

3fro__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of Pyrococcus abyssi glycogen synthase with open and closed conformations

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

GlgA glycogen synthase

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

3fro__assembly_1__model_1

3fro__assembly_1__model_1 | I(q)

3fro__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)