1pyg

STRUCTURAL BASIS FOR THE ACTIVATION OF GLYCOGEN PHOSPHORYLASE B BY ADENOSINE MONOPHOSPHATE

Method: X-RAY DIFFRACTION

▼

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

GLYCOGEN PHOSPHORYLASE B

Oryctolagus cuniculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	ADENOSINE MONOPHOSPHATE × 4 PYRIDOXAL-5'-DIPHOSPHATE × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHS2_RABIT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–842； UniProt 1–842 Author chain B； PDBConstruct 1–842； UniProt 1–842 Author chain C； PDBConstruct 1–842； UniProt 1–842 Author chain D； PDBConstruct 1–842； UniProt 1–842

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1pyg
Deposition date deposition_date	1992-07-07
Structure title title	STRUCTURAL BASIS FOR THE ACTIVATION OF GLYCOGEN PHOSPHORYLASE B BY ADENOSINE MONOPHOSPHATE
Keywords keywords	GLYCOGEN PHOSPHORYLASE; GLYCOGEN PHOSPHORYLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1pyg__assembly_1__model_1

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

Download this curve (.dat)

1pyg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1pyg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	48.63 Å
Rg (electron density)	47.72 Å
Total Rg	48.06 Å
Atom count	26138
Residues	3194
Excluded volume	464710 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1pyg__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	GLYCOGEN PHOSPHORYLASE B
Molecular weight formula_weight	97291.2 kDa
EC 编号 ec_number	2.4.1.1
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	26214

SRPLSDQEKRKQISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRDHLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEATYQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEFGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQGAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLKDFNVGGYIQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSKFGCRDPVRTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEPSRQRLPAPDEKIP

Source Source

Source organism organism	Oryctolagus cuniculus
Common name common_name	rabbit
NCBI taxonomy ID ncbi_taxonomy_id	9986

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	PYRIDOXAL-5'-DIPHOSPHATE
Molecular weight formula_weight	327.1 kDa
Source method src_method	syn
Copy count entity_count	4

▼

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1pyga_
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.87.1.4 — Oligosaccharide phosphorylase

Domain ID domain_id	d1pygb_
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.87.1.4 — Oligosaccharide phosphorylase

Domain ID domain_id	d1pygc_
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.87.1.4 — Oligosaccharide phosphorylase

Domain ID domain_id	d1pygd_
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.87.1.4 — Oligosaccharide phosphorylase

CATH v4.4 (8 domains)

Domain ID domain_id	1pygA01
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	1pygA02
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	1pygB01
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	1pygB02
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	1pygC01
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	1pygC02
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	1pygD01
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	1pygD02
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;

▶

7. Citations (8)

Structural basis for the activation of glycogen phosphorylase b by adenosine monophosphate.

Science (1991)

PMID: 1962195 PRIMARY

;Multiple Phosphate Positions in the Catalytic Site of Glycogen Phosphorylase: Structure of the Pyridoxal-5'-Pyrophosphate Coenzyme-Substrate Analog ;

Protein Sci. (1992)

Domain Separation in the Activation of Glycogen Phosphorylase A

Science (1989)

Structural Changes in Glycogen Phosphorylase Induced by Phosphorylation

Nature (1988)

Structure of the Nucleotide Activation Switch in Glycogen Phosphorylase A

Science (1987)

Catalytic Site of Glycogen Phosphorylase: Structural Changes During Activation and Mechanistic Implications

Biochemistry (1982)

;Evidence for Direct Phosphate-Phosphate Interaction between Pyridoxal Phosphate and Substrate in the Glycogen Phosphorylase Catalytic Mechanism ;

J.Biol.Chem. (1981)

The Structure of Glycogen Phosphorylase a at 2.5 Angstroms Resolution

J.Mol.Biol. (1979)

Unit-cell length a length_a	169.900 Å
Unit-cell length b length_b	209.900 Å
Unit-cell length c length_c	123.400 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	2.870 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.1850
R_free r_free	—

STRUCTURAL BASIS FOR THE ACTIVATION OF GLYCOGEN PHOSPHORYLASE B BY ADENOSINE MONOPHOSPHATE

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

GLYCOGEN PHOSPHORYLASE B

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

1pyg__assembly_1__model_1

1pyg__assembly_1__model_1 | I(q)

1pyg__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (8)

STRUCTURAL BASIS FOR THE ACTIVATION OF GLYCOGEN PHOSPHORYLASE B BY ADENOSINE MONOPHOSPHATE

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

GLYCOGEN PHOSPHORYLASE B

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

1pyg__assembly_1__model_1

1pyg__assembly_1__model_1 | I(q)

1pyg__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (8)