2wvj

Mutation of Thr163 to Ser in Human Thymidine Kinase Shifts the Specificity from Thymidine towards the Nucleoside Analogue Azidothymidine

Method: X-RAY DIFFRACTION

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

THYMIDINE KINASE, CYTOSOLIC

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	THYMIDINE-5'-TRIPHOSPHATE × 4 ZINC ION × 4 MAGNESIUM ION × 1 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	THYMIDINE-5'-TRIPHOSPHATE × 4 ZINC ION × 4 MAGNESIUM ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KITH_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–193； UniProt 1–193 Author chain B； PDBConstruct 1–193； UniProt 1–193 Author chain C； PDBConstruct 1–193； UniProt 1–193 Author chain D； PDBConstruct 1–193； UniProt 1–193 Author chain E； PDBConstruct 1–193； UniProt 1–193 Author chain F； PDBConstruct 1–193； UniProt 1–193 Author chain G； PDBConstruct 1–193； UniProt 1–193 Author chain H； PDBConstruct 1–193； UniProt 1–193

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	2wvj
Deposition date deposition_date	2009-10-17
Structure title title	Mutation of Thr163 to Ser in Human Thymidine Kinase Shifts the Specificity from Thymidine towards the Nucleoside Analogue Azidothymidine
Keywords keywords	;ZINC-BINDING DOMAIN, DEOXYRIBONUCLEOSIDE KINASE, FEEDBACK INHIBITOR, NUCLEOTIDE-BINDING, KINASE, CYTOPLASM, TRANSFERASE, ATP-BINDING, DNA SYNTHESIS, PHOSPHOPROTEIN, PHOSPHORYLATION ;; 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.

2wvj__assembly_1__model_1

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

Download this curve (.dat)

2wvj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2wvj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.24 Å
Rg (electron density)	24.43 Å
Total Rg	25.28 Å
Atom count	5100
Residues	643
Excluded volume	91954 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2wvj__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2wvj__assembly_2__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, CYTOSOLIC
Molecular weight formula_weight	21313.0 kDa
EC 编号 ec_number	2.7.1.21
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	11307

MSCINLPTVLPGSPSKTRGQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSSSFCTHDRNTMEALPACLLRDVAQEALGVAVIGIDEGQFFPDIVEFCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLTAVCMECFREAAYSKRLGTEKEVEVIGGADKYHSVCRLCYFKKA

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	THYMIDINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	482.2 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1074

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d2wvja1
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	d2wvja2
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.39.1.0 — automated matches

Domain ID domain_id	d2wvjb1
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	d2wvjb2
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.39.1.0 — automated matches

Domain ID domain_id	d2wvjc1
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	d2wvjc2
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.39.1.0 — automated matches

Domain ID domain_id	d2wvjd1
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	d2wvjd2
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.39.1.0 — automated matches

Domain ID domain_id	d2wvje1
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	d2wvje2
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.39.1.0 — automated matches

Domain ID domain_id	d2wvjf1
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	d2wvjf2
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.39.1.0 — automated matches

Domain ID domain_id	d2wvjg1
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	d2wvjg2
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.39.1.0 — automated matches

Domain ID domain_id	d2wvjh1
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	d2wvjh2
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.39.1.0 — automated matches

CATH v4.4 (16 domains)

Domain ID domain_id	2wvjA01
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	2wvjA02
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	2wvjB01
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	2wvjB02
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	2wvjC01
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	2wvjC02
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	2wvjD01
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	2wvjD02
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	2wvjE01
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	2wvjE02
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	2wvjF01
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	2wvjF02
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	2wvjG01
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	2wvjG02
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	2wvjH01
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	2wvjH02
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	156.902 Å
Unit-cell length b length_b	123.252 Å
Unit-cell length c length_c	121.024 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	132.98 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	49.814 Å
R factor r_factor	0.1760
R_work r_work	0.1733
R_free r_free	0.2209

Mutation of Thr163 to Ser in Human Thymidine Kinase Shifts the Specificity from Thymidine towards the Nucleoside Analogue Azidothymidine

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

THYMIDINE KINASE, CYTOSOLIC

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

2wvj__assembly_1__model_1

2wvj__assembly_1__model_1 | I(q)

2wvj__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) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)

Mutation of Thr163 to Ser in Human Thymidine Kinase Shifts the Specificity from Thymidine towards the Nucleoside Analogue Azidothymidine

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

THYMIDINE KINASE, CYTOSOLIC

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

2wvj__assembly_1__model_1

2wvj__assembly_1__model_1 | I(q)

2wvj__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) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)