5w6j

Agrobacterium tumefaciens ADP-glucose pyrophosphorylase

Method: X-RAY DIFFRACTION

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

Glucose-1-phosphate adenylyltransferase

Rhizobium radiobacter

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 9 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 8 water × 4	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 8 water × 4	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 8 water × 4	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 9 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLGC_RHIRD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–420； UniProt 1–420 Author chain B； PDBConstruct 1–420； UniProt 1–420 Author chain C； PDBConstruct 1–420； UniProt 1–420 Author chain D； PDBConstruct 1–420； UniProt 1–420 Author chain E； PDBConstruct 1–420； UniProt 1–420 Author chain F； PDBConstruct 1–420； UniProt 1–420 Author chain G； PDBConstruct 1–420； UniProt 1–420 Author chain H； PDBConstruct 1–420； UniProt 1–420 Author chain I； PDBConstruct 1–420； UniProt 1–420 Author chain J； PDBConstruct 1–420； UniProt 1–420 Author chain K； PDBConstruct 1–420； UniProt 1–420 Author chain L； PDBConstruct 1–420； UniProt 1–420 Author chain M； PDBConstruct 1–420； UniProt 1–420 Author chain N； PDBConstruct 1–420； UniProt 1–420 Author chain O； PDBConstruct 1–420； UniProt 1–420 Author chain P； PDBConstruct 1–420； UniProt 1–420 Author chain Q； PDBConstruct 1–420； UniProt 1–420 Author chain R； PDBConstruct 1–420； UniProt 1–420 Author chain T； PDBConstruct 1–420； UniProt 1–420 Author chain U； PDBConstruct 1–420； UniProt 1–420

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	5w6j
Deposition date deposition_date	2017-06-16
Structure title title	Agrobacterium tumefaciens ADP-glucose pyrophosphorylase
Keywords keywords	Glucose-1-phosphate adenylyltransferase, glycogen biosynthesis, starch biosynthesis, allosterism, 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.

5w6j__assembly_1__model_1

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

Download this curve (.dat)

5w6j__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5w6j__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.15 Å
Rg (electron density)	34.89 Å
Total Rg	35.54 Å
Atom count	12909
Residues	1644
Excluded volume	228150 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5w6j__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5w6j__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5w6j__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5w6j__assembly_4__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`5w6j__assembly_5__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	Glucose-1-phosphate adenylyltransferase
Molecular weight formula_weight	47101.2 kDa
EC 编号 ec_number	2.7.7.27
Source method src_method	man
Copy count entity_count	20

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,H,I,J,K,L,N,O,P,Q,R,F,G,M,T,U
Atom count atom_count	75925

MSEKRVQPLARDAMAYVLAGGRGSRLKELTDRRAKPAVYFGGKARIIDFALSNALNSGIRRIGVATQYKAHSLIRHLQRGWDFFRPERNESFDILPASQRVSETQWYEGTADAVYQNIDIIEPYAPEYMVILAGDHIYKMDYEYMLQQHVDSGADVTIGCLEVPRMEATGFGVMHVNEKDEIIDFIEKPADPPGIPGNEGFALASMGIYVFHTKFLMEALRRDAADPTSSRDFGKDIIPYIVEHGKAVAHRFADSCVRSDFEHEPYWRDVGTIDAYWQANIDLTDVVPDLDIYDKSWPIWTYAEITPPAKFVHDDEDRRGSAVSSVVSGDCIISGAALNRSLLFTGVRANSYSRLENAVVLPSVKIGRHAQLSNVVIDHGVVIPEGLIVGEDPELDAKRFRRTESGICLITQSMIDKLDL

Source Source

Source organism organism	Rhizobium radiobacter
Common name common_name	Agrobacterium tumefaciens
NCBI taxonomy ID ncbi_taxonomy_id	358
Host organism host_organism	Escherichia coli K-12

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	42

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	11196

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6. Fold Classification (SCOP + CATH) 40 domains

CATH v4.4 (40 domains)

Domain ID domain_id	5w6jA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	5w6jA02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	5w6jB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	5w6jB02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	5w6jC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	5w6jC02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	5w6jD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	5w6jD02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	5w6jE01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	5w6jE02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	5w6jF01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	5w6jF02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	5w6jG01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	5w6jG02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	5w6jH01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	5w6jH02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	5w6jI01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	5w6jI02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	5w6jJ01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	5w6jJ02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	5w6jK01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	5w6jK02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	5w6jL01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	5w6jL02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	5w6jM01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	5w6jM02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	5w6jN01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	5w6jN02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	5w6jO01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	5w6jO02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	5w6jP01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	5w6jP02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	5w6jQ01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	5w6jQ02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	5w6jR01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	5w6jR02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	5w6jT01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	5w6jT02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

Domain ID domain_id	5w6jU01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	5w6jU02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

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Unit-cell length a length_a	93.439 Å
Unit-cell length b length_b	140.685 Å
Unit-cell length c length_c	228.490 Å
Unit-cell angle α angle_alpha	72.04 °
Unit-cell angle β angle_beta	78.19 °
Unit-cell angle γ angle_gamma	89.98 °
Molecules per unit cell Z z_pdb	20

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.780 Å
Low-resolution limit resolution_low	36.550 Å
R factor r_factor	0.2020
R_work r_work	0.2000
R_free r_free	0.2290

Agrobacterium tumefaciens ADP-glucose pyrophosphorylase

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

Glucose-1-phosphate adenylyltransferase

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

5w6j__assembly_1__model_1

5w6j__assembly_1__model_1 | I(q)

5w6j__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 40 domains

CATH v4.4 (40 domains)

7. Citations (1)

Agrobacterium tumefaciens ADP-glucose pyrophosphorylase

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

Glucose-1-phosphate adenylyltransferase

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

5w6j__assembly_1__model_1

5w6j__assembly_1__model_1 | I(q)

5w6j__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 40 domains

CATH v4.4 (40 domains)

7. Citations (1)