SAXSdb — 2dei

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

Probable galactokinase

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	alpha-D-galactopyranose × 1 MAGNESIUM-5'-ADENYLY-IMIDO-TRIPHOSPHATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GAL1_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–350； UniProt 1–350

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	2dei
Deposition date deposition_date	2006-02-10
Structure title title	Crystal Structure of galaktokinase from Pyrococcus horikoshii with AMP-PNP and galactose
Keywords keywords	;galactokinase, ATP analogue, galactose, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, 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.

2dei__assembly_1__model_1

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

Download this curve (.dat)

2dei__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dei__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.17 Å
Rg (electron density)	20.27 Å
Total Rg	21.18 Å
Atom count	2816
Residues	350
Excluded volume	50361 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dei__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	Probable galactokinase
Molecular weight formula_weight	39397.0 kDa
EC 编号 ec_number	2.7.1.6
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	3152

MIKVKSPGRVNLIGEHTDYTYGYVMPMAINLYTKIEAEKHGEVILYSEHFGEERKFSLNDLRKENSWIDYVKGIFWVLKESDYEVGGIKGRVSGNLPLGAGLSSSASFEVGILETLDKLYNLKLDSLSKVLLAKKAENEFVGVPCGILDQFAVVFGREGNVIFLDTHTLDYEYIPFPKDVSILVFYTGVRRELASSEYAERKHIAEESLKILGKGSSKEVREGELSKLPPLHRKFFGYIVRENARVLEVRDALKEGNVEEVGKILTTAHWDLAKNYEVSCKELDFFVERALKLGAYGARLTGAGFGGSAIALVDKEDAETIGEEILREYLKRFPWKARHFIVEPSDGVGI

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	53953
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM-5'-ADENYLY-IMIDO-TRIPHOSPHATE
Molecular weight formula_weight	529.5 kDa
Source method src_method	syn
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	287

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2deia1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.0 — automated matches

Domain ID domain_id	d2deia2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.26 — GHMP Kinase, C-terminal domain
Family Family family	d.58.26.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2deiA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2deiA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	890 — GHMP kinase, C-terminal domain

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Unit-cell length a length_a	106.333 Å
Unit-cell length b length_b	39.067 Å
Unit-cell length c length_c	81.418 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.50 °
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	1.700 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.1790
R_work r_work	0.1767
R_free r_free	0.2213

Crystal Structure of galaktokinase from Pyrococcus horikoshii with AMP-PNP and galactose

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

Probable galactokinase

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

2dei__assembly_1__model_1

2dei__assembly_1__model_1 | I(q)

2dei__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of galaktokinase from Pyrococcus horikoshii with AMP-PNP and galactose

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

Probable galactokinase

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

2dei__assembly_1__model_1

2dei__assembly_1__model_1 | I(q)

2dei__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)