1wye

Crystal structure of 2-keto-3-deoxygluconate kinase (form 1) from Sulfolobus Tokodaii

Method: X-RAY DIFFRACTION

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

2-keto-3-deoxygluconate kinase

Sulfolobus tokodaii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q96XN9_SULTO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–311； UniProt 1–311 Author chain B； PDBConstruct 1–311； UniProt 1–311 Author chain C； PDBConstruct 1–311； UniProt 1–311 Author chain D； PDBConstruct 1–311； UniProt 1–311 Author chain E； PDBConstruct 1–311； UniProt 1–311 Author chain F； PDBConstruct 1–311； UniProt 1–311

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	1wye
Deposition date deposition_date	2005-02-12
Structure title title	Crystal structure of 2-keto-3-deoxygluconate kinase (form 1) from Sulfolobus Tokodaii
Keywords keywords	archea, Sulfolobus tokokai, 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.

1wye__assembly_1__model_1

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

Download this curve (.dat)

1wye__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1wye__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.48 Å
Rg (electron density)	35.81 Å
Total Rg	36.44 Å
Atom count	14456
Residues	1854
Excluded volume	258990 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1wye__assembly_1__model_1`	hexameric （6）	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 (2)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1wyea_
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.72.1.0 — automated matches

Domain ID domain_id	d1wyeb_
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.72.1.0 — automated matches

Domain ID domain_id	d1wyec_
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.72.1.0 — automated matches

Domain ID domain_id	d1wyed_
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.72.1.0 — automated matches

Domain ID domain_id	d1wyee_
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.72.1.0 — automated matches

Domain ID domain_id	d1wyef_
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.72.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	1wyeA00
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	1wyeB00
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	1wyeC00
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	1wyeD00
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	1wyeE00
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	1wyeF00
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

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Unit-cell length a length_a	84.666 Å
Unit-cell length b length_b	149.103 Å
Unit-cell length c length_c	161.096 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	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1881
R_work r_work	0.1789
R_free r_free	0.2705

Description description	2-keto-3-deoxygluconate kinase
Molecular weight formula_weight	34523.3 kDa
EC 编号 ec_number	2.7.1.45
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	14836

Crystal structure of 2-keto-3-deoxygluconate kinase (form 1) from Sulfolobus Tokodaii

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

2-keto-3-deoxygluconate kinase

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

1wye__assembly_1__model_1

1wye__assembly_1__model_1 | I(q)

1wye__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Source organism organism	Sulfolobus tokodaii
NCBI taxonomy ID ncbi_taxonomy_id	273063
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	380

Crystal structure of 2-keto-3-deoxygluconate kinase (form 1) from Sulfolobus Tokodaii

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

2-keto-3-deoxygluconate kinase

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

1wye__assembly_1__model_1

1wye__assembly_1__model_1 | I(q)

1wye__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)