1p75

Crystal structure of EHV4-TK complexed with TP5A

Method: X-RAY DIFFRACTION

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

Thymidine kinase

Equid herpesvirus 4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 12 P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 4 P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 8	SULFATE ION × 32 P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE × 8 water × 8	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 16 P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KITH_EHV4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–334； UniProt 23–352 Author chain B； PDBConstruct 5–334； UniProt 23–352 Author chain C； PDBConstruct 5–334； UniProt 23–352 Author chain D； PDBConstruct 5–334； UniProt 23–352

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	1p75
Deposition date deposition_date	2003-04-30
Structure title title	Crystal structure of EHV4-TK complexed with TP5A
Keywords keywords	P-loop, Lid, 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.

1p75__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1p75__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1p75__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	26.16 Å
Rg (electron density)	24.71 Å
Total Rg	25.61 Å
Atom count	5183
Residues	658
Excluded volume	91606 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1p75__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1p75__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1p75__assembly_3__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1p75__assembly_4__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 (4)

Entity 1 Entity 1 polymer

Description description	Thymidine kinase
Molecular weight formula_weight	37013.3 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	10704

GSHMVTIVRIYLDGVYGIGKSTTGRVMASAASGGSPTLYFPEPMAYWRTLFETDVISGIYDTQNRKQQGNLAVDDAALITAHYQSRFTTPYLILHDHTCTLFGGNSLQRGTQPDLTLVFDRHPVASTVCFPAARYLLGDMSMCALMAMVATLPREPQGGNIVVTTLNVEEHIRRLRTRARIGEQIDITLIATLRNVYFMLVNTCHFLRSGRVWRDGWGELPTSCGAYKHRATQMDAFQERVSPELGDTLFALFKTQELLDDRGVILEVHAWALDALMLKLRNLNVFSADLSGTPRQCAAVVESLLPLMSSTLSDFDSASALERAARTFNAEMGV

Source Source

Source organism organism	Equid herpesvirus 4
Common name common_name	Equine herpesvirus 4
NCBI taxonomy ID ncbi_taxonomy_id	10331
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 3 Entity 3 non-polymer

Description description	P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE
Molecular weight formula_weight	891.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	155

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1p75a1
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.37.1.1 — Nucleotide and nucleoside kinases

Domain ID domain_id	d1p75a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1p75b1
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.37.1.1 — Nucleotide and nucleoside kinases

Domain ID domain_id	d1p75b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1p75c1
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.37.1.1 — Nucleotide and nucleoside kinases

Domain ID domain_id	d1p75c2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1p75d1
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.37.1.1 — Nucleotide and nucleoside kinases

Domain ID domain_id	d1p75d2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	1p75A00
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	1p75B00
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	1p75C00
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	1p75D00
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

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Unit-cell length a length_a	106.874 Å
Unit-cell length b length_b	117.227 Å
Unit-cell length c length_c	125.003 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	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.020 Å
Low-resolution limit resolution_low	29.580 Å
R factor r_factor	0.2111
R_work r_work	0.2018
R_free r_free	0.2977

Crystal structure of EHV4-TK complexed with TP5A

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

1p75__assembly_2__model_1

1p75__assembly_2__model_1 | I(q)

1p75__assembly_2__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) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of EHV4-TK complexed with TP5A

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

1p75__assembly_2__model_1

1p75__assembly_2__model_1 | I(q)

1p75__assembly_2__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) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)