SAXSdb — 5o0j

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

ADP-dependent glucokinase

Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	8-BROMO-ADENOSINE-5'-MONOPHOSPHATE × 2 alpha-D-glucopyranose × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLKA_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–453； UniProt 5–457

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	5o0j
Deposition date deposition_date	2017-05-16
Structure title title	ADP-dependent glucokinase from Pyrococcus horikoshii
Keywords keywords	ADP-dependent glucokinase, 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.

5o0j__assembly_1__model_1

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

Download this curve (.dat)

5o0j__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5o0j__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.42 Å
Rg (electron density)	21.34 Å
Total Rg	22.31 Å
Atom count	3706
Residues	453
Excluded volume	66577 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5o0j__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	ADP-dependent glucokinase
Molecular weight formula_weight	51689.6 kDa
EC 编号 ec_number	2.7.1.147
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4238

TNWESLYEKALDKVEASIRKVRGVLLAYNTNIDAIKYLKREDLEKRIEKVGKEEVLRYSEELPKEIETIPQLLGSILWSIKRGKAAELLVVSREVREYMRKWGWDELRMGGQVGIMANLLGGVYGIPVIAHVPQLSELQASLFLDGPIYVPTFERGELRLIHPREFRKGEEDCIHYIYEFPRNFKVLDFEAPRENRFIGAADDYNPILYVREEWIERFEEIAKRSELAIISGLHPLTQENHGKPIKLVREHLKILNDLGIRAHLEFAFTPDEVVRLEIVKLLKHFYSVGLNEVELASVVSVMGEKELAERIISKDPADPIAVIEGLLKLIKETGVKRIHFHTYGYYLALTREKGEHVRDALLFSALAAATKAMKGNIEKLSDIREGLAVPIGEQGLEVEKILEKEFSLRDGIGSIEDYQLTFIPTKVVKKPKSTVGIGDTISSSAFVSEFSLH

Source Source

Source organism organism	Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
NCBI taxonomy ID ncbi_taxonomy_id	70601
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	8-BROMO-ADENOSINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	426.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	alpha-D-glucopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	522

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5o0ja_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.72 — Ribokinase-like
Superfamily Superfamily superfamily	c.72.1 — Ribokinase-like
Family Family family	c.72.1.3 — ADP-specific Phosphofructokinase/Glucokinase

CATH v4.4 (2 domains)

Domain ID domain_id	5o0jA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Homologous superfamily homologous superfamily	20 — Ribokinase

Domain ID domain_id	5o0jA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1110 — Adenosine kinase, small domain
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	115.838 Å
Unit-cell length b length_b	74.714 Å
Unit-cell length c length_c	62.951 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.46 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.810 Å
Low-resolution limit resolution_low	45.977 Å
R factor r_factor	0.1626
R_work r_work	0.1608
R_free r_free	0.2019

ADP-dependent glucokinase from Pyrococcus horikoshii

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

ADP-dependent glucokinase

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

5o0j__assembly_1__model_1

5o0j__assembly_1__model_1 | I(q)

5o0j__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

ADP-dependent glucokinase from Pyrococcus horikoshii

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

ADP-dependent glucokinase

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

5o0j__assembly_1__model_1

5o0j__assembly_1__model_1 | I(q)

5o0j__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)