3zvm

The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase

Method: X-RAY DIFFRACTION

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

BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 1	5'-D(GPTPCPAP*CP)-3' × 1 ADENOSINE-5'-DIPHOSPHATE × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 MAGNESIUM ION × 2 GLYCEROL × 4 ACETATE ION × 2 water × 2	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 1	5'-D(GPTPCPAP*CP)-3' × 1 ADENOSINE-5'-DIPHOSPHATE × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 MAGNESIUM ION × 2 GLYCEROL × 4 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PNKP_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–416； UniProt 111–522 Author chain B； PDBConstruct 5–416； UniProt 111–522

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	3zvm
Deposition date deposition_date	2011-07-25
Structure title title	The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase
Keywords keywords	HYDROLASE-TRANSFERASE-DNA COMPLEX, BASE EXCISION REPAIR, BER, NON-HOMOLOGOUS END-JOINING, NHEJ, DNA REPAIR, CANCER; HYDROLASE/TRANSFERASE/DNA
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.

3zvm__assembly_2__model_1

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

Download this curve (.dat)

3zvm__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3zvm__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	25.45 Å
Rg (electron density)	25.26 Å
Total Rg	25.95 Å
Atom count	3091
Residues	384
Excluded volume	54929 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3zvm__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3zvm__assembly_2__model_1`	dimeric （2）	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 (8)

Entity 1 Entity 1 polymer

Description description	BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE
Molecular weight formula_weight	45932.2 kDa
EC 编号 ec_number	3.1.3.32, 2.7.1.78
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7426

GPHMTSGSQPDAPPDTPGDPEEGEDTEPQKKRVRKSSLGWESLKKLLVFTASGVKPQGKVAAFDLDGTLITTRSGKVFPTSPSDWRILYPEIPKKLQELAAEGYKLVIFTNQMGIGRGKLPAEVFKGKVEAVLEKLGVPFQVLVATHAGLNRKPVSGMWDHLQEQANEGIPISVEDSVFVGDAAGRLANWAPGRKKKDFSCADRLFALNVGLPFATPEEFFLKWPAARFELPAFDPRTISSAGPLYLPESSSLLSPNPEVVVAVGFPGAGKSTFIQEHLVSAGYVHVNRDTLGSWQRCVSSCQAALRQGKRVVIDNTNPDVPSRARYIQCAKDAGVPCRCFNFCATIEQARHNNRFREMTDPSHAPVSDMVMFSYRKQFEPPTLAEGFLEILEIPFRLQEHLDPALQRLYRQFSEG

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	5'-D(GPTPCPAP*CP)-3'
Molecular weight formula_weight	1480.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,F

GTCAC

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 7 Entity 7 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1196

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3zvmA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	3zvmA02
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	3zvmB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	3zvmB02
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	44.817 Å
Unit-cell length b length_b	75.243 Å
Unit-cell length c length_c	135.199 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.997 Å
Low-resolution limit resolution_low	38.490 Å
R factor r_factor	0.1545
R_work r_work	0.1520
R_free r_free	0.2006

The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase

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

BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/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

3zvm__assembly_2__model_1

3zvm__assembly_2__model_1 | I(q)

3zvm__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase

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

BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/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

3zvm__assembly_2__model_1

3zvm__assembly_2__model_1 | I(q)

3zvm__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)