SAXSdb — 2v4y

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

URIDYLATE KINASE

ESCHERICHIA COLI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	GUANOSINE-5'-TRIPHOSPHATE × 12 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYRH_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–241； UniProt 1–241 Author chain B； PDBConstruct 1–241； UniProt 1–241 Author chain C； PDBConstruct 1–241； UniProt 1–241 Author chain D； PDBConstruct 1–241； UniProt 1–241 Author chain E； PDBConstruct 1–241； UniProt 1–241 Author chain F； PDBConstruct 1–241； UniProt 1–241

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	2v4y
Deposition date deposition_date	2008-09-30
Structure title title	THE STRUCTURE OF E. COLI UMP KINASE IN COMPLEX WITH ITS ALLOSTERIC REGULATOR GTP
Keywords keywords	NUCLEOTIDE-BINDING, PYRIMIDINE BIOSYNTHESIS, TRANSFERASE, ATP-BINDING, ALLOSTERIC ENZYME, GTP, KINASE, ALLOSTERY, NMP KINASE; 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.

2v4y__assembly_1__model_1

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

Download this curve (.dat)

2v4y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2v4y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.10 Å
Rg (electron density)	32.57 Å
Total Rg	33.09 Å
Atom count	10895
Residues	1407
Excluded volume	194590 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2v4y__assembly_1__model_1`	hexameric （6）	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 (3)

Entity 1 Entity 1 polymer

Description description	URIDYLATE KINASE
Molecular weight formula_weight	25999.3 kDa
EC 编号 ec_number	2.7.4.22
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	10907

MATNAKPVYKRILLKLSGEALQGTEGFGIDASILDRMAQEIKELVELGIQVGVVIGGGNLFRGAGLAKAGMNRVVGDHMGMLATVMNGLAMRDALHRAYVNARLMSAIPLNGVCDSYSWAEAISLLRNNRVVILSAGTGNPFFTTDSAACLRGIEIEANVVLKATKVDGVFTADPAKDPTATMYEQLTYSEVLEKELKVMDLAAFTLARDHKLPIRVFNMNKPGALRRVVMGEKEGTLITE

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	12

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2v4ya_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.73 — Carbamate kinase-like
Superfamily Superfamily superfamily	c.73.1 — Carbamate kinase-like
Family Family family	c.73.1.3 — PyrH-like

Domain ID domain_id	d2v4yb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.73 — Carbamate kinase-like
Superfamily Superfamily superfamily	c.73.1 — Carbamate kinase-like
Family Family family	c.73.1.3 — PyrH-like

Domain ID domain_id	d2v4yc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.73 — Carbamate kinase-like
Superfamily Superfamily superfamily	c.73.1 — Carbamate kinase-like
Family Family family	c.73.1.3 — PyrH-like

Domain ID domain_id	d2v4yd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.73 — Carbamate kinase-like
Superfamily Superfamily superfamily	c.73.1 — Carbamate kinase-like
Family Family family	c.73.1.3 — PyrH-like

Domain ID domain_id	d2v4ye_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.73 — Carbamate kinase-like
Superfamily Superfamily superfamily	c.73.1 — Carbamate kinase-like
Family Family family	c.73.1.3 — PyrH-like

Domain ID domain_id	d2v4yf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.73 — Carbamate kinase-like
Superfamily Superfamily superfamily	c.73.1 — Carbamate kinase-like
Family Family family	c.73.1.3 — PyrH-like

CATH v4.4 (6 domains)

Domain ID domain_id	2v4yA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	2v4yB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	2v4yC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	2v4yD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	2v4yE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	2v4yF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

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Unit-cell length a length_a	66.280 Å
Unit-cell length b length_b	145.780 Å
Unit-cell length c length_c	146.600 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	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	49.038 Å
R factor r_factor	0.2090
R_work r_work	0.2074
R_free r_free	0.2387

THE STRUCTURE OF E. COLI UMP KINASE IN COMPLEX WITH ITS ALLOSTERIC REGULATOR GTP

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

URIDYLATE 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

2v4y__assembly_1__model_1

2v4y__assembly_1__model_1 | I(q)

2v4y__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

THE STRUCTURE OF E. COLI UMP KINASE IN COMPLEX WITH ITS ALLOSTERIC REGULATOR GTP

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

URIDYLATE 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

2v4y__assembly_1__model_1

2v4y__assembly_1__model_1 | I(q)

2v4y__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)