SAXSdb — 4kx3

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

;Isoform 1 of Cytosolic 5'-nucleotidase 3A ;

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	THYMIDINE-5'-PHOSPHATE × 1 MAGNESIUM ION × 1 1,2-ETHANEDIOL × 4 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	5NT3A_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–297； UniProt 1–297

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	4kx3
Deposition date deposition_date	2013-05-24
Structure title title	Structure of murine cytosolic 5'-nucleotidase III complexed with thymidine monophosphate
Keywords keywords	;SUBSTRATE COMPLEX, HAD SUPERFAMILY, NUCLEOTIDASE, UMPH-1, CYTOSOLIC 5'-NUCLEOTIDASE III, P5N-1, HYDROLASE ;; HYDROLASE
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.

4kx3__assembly_1__model_1

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

Download this curve (.dat)

4kx3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4kx3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.22 Å
Rg (electron density)	19.07 Å
Total Rg	20.13 Å
Atom count	2387
Residues	289
Excluded volume	42947 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4kx3__assembly_1__model_1`	monomeric （1）	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 (6)

Entity 1 Entity 1 polymer

Description description	;Isoform 1 of Cytosolic 5'-nucleotidase 3A ;
Molecular weight formula_weight	33940.0 kDa
EC 编号 ec_number	3.1.3.5,3.1.3.91
Mutation mutation	D51N, M1S
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	2645

STNQESAVHLKMMPEFQKSSVRIKNPTRVEEIICGLIKGGAAKLQIITDFNMTLSRFSYNGKRCPTCHNIIDNCKLVTDECRRKLLQLKEQYYAIEVDPVLTVEEKFPYMVEWYTKSHGLLIEQGIPKAKLKEIVADSDVMLKEGYENFFGKLQQHGIPVFIFSAGIGDVLEEVIRQAGVYHSNVKVVSNFMDFDENGVLKGFKGELIHVFNKHDGALKNTDYFSQLKDNSNIILLGDSQGDLRMADGVANVEHILKIGYLNDRVDELLEKYMDSYDIVLVKEESLEVVNSILQKTL

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	THYMIDINE-5'-PHOSPHATE
Molecular weight formula_weight	322.2 kDa
Source method src_method	syn
Copy count entity_count	1

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	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 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	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	246

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4kx3a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.21 — Pyrimidine 5'-nucleotidase (UMPH-1)

CATH v4.4 (2 domains)

Domain ID domain_id	4kx3A01
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	4kx3A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	340 — Pyrimidine 5'-nucleotidase (UMPH-1), N-terminal domain

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Unit-cell length a length_a	46.872 Å
Unit-cell length b length_b	46.872 Å
Unit-cell length c length_c	285.873 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	8

Space group space_group	P 43 2 2
Space-group number int_tables_number	95
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	46.920 Å
R factor r_factor	0.1561
R_work r_work	0.1531
R_free r_free	0.2165

Structure of murine cytosolic 5'-nucleotidase III complexed with thymidine monophosphate

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

;Isoform 1 of Cytosolic 5'-nucleotidase 3A ;

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

4kx3__assembly_1__model_1

4kx3__assembly_1__model_1 | I(q)

4kx3__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) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of murine cytosolic 5'-nucleotidase III complexed with thymidine monophosphate

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

;Isoform 1 of Cytosolic 5'-nucleotidase 3A ;

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

4kx3__assembly_1__model_1

4kx3__assembly_1__model_1 | I(q)

4kx3__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) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)