SAXSdb — 1uke

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

URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE KINASE

Dictyostelium discoideum

UniProt P20425

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 P1-(ADENOSINE-5'-P5-(URIDINE-5')PENTAPHOSPHATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KCY_DICDI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–194； UniProt 1–194

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	1uke
Deposition date deposition_date	1998-01-07
Structure title title	UMP/CMP KINASE FROM SLIME MOLD
Keywords keywords	NMP KINASE, NUCLEOTIDE SPECIFICITY, PHOSPHORYL TRANSFER, BISUBSTRATE INHIBITOR, NUCLEOTIDE MONOPHOSPHATE KINASE; NUCLEOTIDE MONOPHOSPHATE KINASE
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.

1uke__assembly_1__model_1

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

Download this curve (.dat)

1uke__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1uke__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.21 Å
Rg (electron density)	16.17 Å
Total Rg	17.14 Å
Atom count	1970
Residues	193
Excluded volume	27909 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1uke__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 (4)

Entity 1 Entity 1 polymer

Description description	URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE KINASE
Molecular weight formula_weight	21970.9 kDa
EC 编号 ec_number	2.7.4.14
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	2099

MEKSKPNVVFVLGGPGSGKGTQCANIVRDFGWVHLSAGDLLRQEQQSGSKDGEMIATMIKNGEIVPSIVTVKLLKNAIDANQGKNFLVDGFPRNEENNNSWEENMKDFVDTKFVLFFDCPEEVMTQRLLKRGESSGRSDDNIESIKKRFNTFNVQTKLVIDHYNKFDKVKIIPANRDVNEVYNDVENLFKSMGF

Source Source

Source organism organism	Dictyostelium discoideum
NCBI taxonomy ID ncbi_taxonomy_id	44689
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	P1-(ADENOSINE-5'-P5-(URIDINE-5')PENTAPHOSPHATE
Molecular weight formula_weight	893.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	43

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ukea_
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

CATH v4.4 (1 domains)

Domain ID domain_id	1ukeA00
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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7. Citations (6)

;Crystal structure of the complex of UMP/CMP kinase from Dictyostelium discoideum and the bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-uridyl) pentaphosphate (UP5A) and Mg2+ at 2.2 A: implications for water-mediated specificity. ;

Biochemistry (1996)

PMID: 8703943 · DOI: 10.1021/bi960642s PRIMARY

High-Resolution Structures of Adenylate Kinase from Yeast Ligated with Inhibitor Ap5A, Showing the Pathway of Phosphoryl Transfer

Protein Sci. (1995)

Movie of the Structural Changes During a Catalytic Cycle of Nucleoside Monophosphate Kinases

Structure (1995)

Substrate Specificity and Assembly of the Catalytic Center Derived from Two Structures of Ligated Uridylate Kinase

J.Mol.Biol. (1995)

;Crystallization and Preliminary X-Ray Analysis of Ump/Cmp-Kinase from Dictyostelium Discoideum with the Specific Bisubstrate Inhibitor P1-(Adenosine 5')-P5-(Uridine 5')-Pentaphosphate (Up5A) ;

FEBS Lett. (1995)

Cdna-Derived Sequence of Ump-Cmp Kinase from Dictyostelium Discoideum and Expression of the Enzyme in Escherichia Coli

J.Biol.Chem. (1990)

Unit-cell length a length_a	78.500 Å
Unit-cell length b length_b	78.500 Å
Unit-cell length c length_c	101.500 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2150
R_work r_work	0.2150
R_free r_free	0.2760

UMP/CMP KINASE FROM SLIME MOLD

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

URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE 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

1uke__assembly_1__model_1

1uke__assembly_1__model_1 | I(q)

1uke__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 (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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (6)

UMP/CMP KINASE FROM SLIME MOLD

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

URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE 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

1uke__assembly_1__model_1

1uke__assembly_1__model_1 | I(q)

1uke__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 (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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (6)