SAXSdb — 3zvl

▼

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 monomer	Monomer	Protein 1	GLYCEROL × 6 MAGNESIUM ION × 1 CHLORIDE ION × 4 ACETATE ION × 4 water × 1	Consistent with protein count

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

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3zvl
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 COMPLEX, BASE EXCISION REPAIR, BER, NON-HOMOLOGOUS END-JOINING, NHEJ, DNA REPAIR, CANCER; HYDROLASE/TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3zvl__assembly_1__model_1

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

Download this curve (.dat)

3zvl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3zvl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.11 Å
Rg (electron density)	25.74 Å
Total Rg	26.44 Å
Atom count	2973
Residues	379
Excluded volume	53047 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3zvl__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE
Molecular weight formula_weight	45948.2 kDa
EC 编号 ec_number	3.1.3.32, 2.7.1.78
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3536

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

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	508

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3zvlA01
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	3zvlA02
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

▶

Unit-cell length a length_a	42.750 Å
Unit-cell length b length_b	63.500 Å
Unit-cell length c length_c	67.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.82 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	33.933 Å
R factor r_factor	0.1729
R_work r_work	0.1705
R_free r_free	0.2182

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

3zvl__assembly_1__model_1

3zvl__assembly_1__model_1 | I(q)

3zvl__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 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

3zvl__assembly_1__model_1

3zvl__assembly_1__model_1 | I(q)

3zvl__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)