2b8t

Crystal structure of Thymidine Kinase from U.urealyticum in complex with thymidine

Method: X-RAY DIFFRACTION

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

Thymidine kinase

Ureaplasma parvum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 4 THYMIDINE × 4 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KITH_UREPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–223； UniProt 1–223 Author chain B； PDBConstruct 1–223； UniProt 1–223 Author chain C； PDBConstruct 1–223； UniProt 1–223 Author chain D； PDBConstruct 1–223； UniProt 1–223

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	2b8t
Deposition date deposition_date	2005-10-10
Structure title title	Crystal structure of Thymidine Kinase from U.urealyticum in complex with thymidine
Keywords keywords	DEOXYRIBONUCLEOSIDE KINASE, ZINC-BINDING DOMAIN, TK1, UU-TK, THYMIDINE, 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.

2b8t__assembly_1__model_1

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

Download this curve (.dat)

2b8t__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2b8t__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.45 Å
Rg (electron density)	27.03 Å
Total Rg	27.91 Å
Atom count	6460
Residues	798
Excluded volume	115400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2b8t__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	Thymidine kinase
Molecular weight formula_weight	25440.2 kDa
EC 编号 ec_number	2.7.1.21
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	6690

MAKVNAFSKKIGWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQFFDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITKLTAICNECGAEATHSLRKIDGKHADYNDDIVKIGCQEFYSAVCRHHHKVPNRPYLNSNSEEFIKFFKNKKRNKNI

Source Source

Source organism organism	Ureaplasma parvum
NCBI taxonomy ID ncbi_taxonomy_id	134821
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	THYMIDINE
Molecular weight formula_weight	242.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	230

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2b8ta1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.24 — Type II thymidine kinase

Domain ID domain_id	d2b8ta2
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.14 — Type II thymidine kinase zinc finger

Domain ID domain_id	d2b8tb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.24 — Type II thymidine kinase

Domain ID domain_id	d2b8tb2
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.14 — Type II thymidine kinase zinc finger

Domain ID domain_id	d2b8tc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.24 — Type II thymidine kinase

Domain ID domain_id	d2b8tc2
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.14 — Type II thymidine kinase zinc finger

Domain ID domain_id	d2b8td1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.24 — Type II thymidine kinase

Domain ID domain_id	d2b8td2
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.14 — Type II thymidine kinase zinc finger

CATH v4.4 (8 domains)

Domain ID domain_id	2b8tA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2b8tA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2b8tB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2b8tB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2b8tC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2b8tC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2b8tD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2b8tD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	57.158 Å
Unit-cell length b length_b	115.649 Å
Unit-cell length c length_c	64.474 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.02 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	26.950 Å
R factor r_factor	0.1974
R_work r_work	0.1953
R_free r_free	0.2350

Crystal structure of Thymidine Kinase from U.urealyticum in complex with thymidine

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

Thymidine 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

2b8t__assembly_1__model_1

2b8t__assembly_1__model_1 | I(q)

2b8t__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of Thymidine Kinase from U.urealyticum in complex with thymidine

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

Thymidine 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

2b8t__assembly_1__model_1

2b8t__assembly_1__model_1 | I(q)

2b8t__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)