SAXSdb — 2bnd

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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	URIDINE-5'-DIPHOSPHATE × 6 GLYCEROL × 15 PYROPHOSPHATE 2- × 3 water × 6	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 2–241； UniProt 1–240 Author chain B； PDBConstruct 2–241； UniProt 1–240

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	2bnd
Deposition date deposition_date	2005-03-23
Structure title title	The structure of E. coli UMP kinase in complex with UDP
Keywords keywords	TRANSFERASE, NUCLEOSIDE MONOPHOSPHATE KINASE, PYRIMIDINE BIOSYNTHESIS; 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.

2bnd__assembly_1__model_1

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

Download this curve (.dat)

2bnd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2bnd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.30 Å
Rg (electron density)	32.64 Å
Total Rg	33.19 Å
Atom count	11004
Residues	1422
Excluded volume	197480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2bnd__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 (5)

Entity 1 Entity 1 polymer

Description description	URIDYLATE KINASE
Molecular weight formula_weight	26013.3 kDa
EC 编号 ec_number	2.7.4.4
Mutation mutation	YES
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	3761

MATNAKPVYKRILLKLSGEALQGTEGFGIDASILDRMAQEIKELVELGIQVGVVIGGGNLFRGAGLAKAGMNRVVGDHMGMLATVMNGLAMRDALHRAYVNARLMSAIPLNAVCDSYSWAEAISLLRNNRVVILSAGTGNPFFTTDSAACLRGIEIEANVVLKATKVDGVFTADPAKDPTATMYEQLTYSEVLEKELKVMDLAAFTLARDHKLPIRVFNMNKPGALRRVVMGEKEGTLITE

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	URIDINE-5'-DIPHOSPHATE
Molecular weight formula_weight	404.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	PYROPHOSPHATE 2-
Molecular weight formula_weight	176.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	93

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2bnda1
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	d2bndb_
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 (2 domains)

Domain ID domain_id	2bndA00
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	2bndB00
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	140.434 Å
Unit-cell length b length_b	140.434 Å
Unit-cell length c length_c	59.993 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	22.500 Å
R factor r_factor	0.1948
R_work r_work	0.1948
R_free r_free	0.2749

The structure of E. coli UMP kinase in complex with UDP

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

2bnd__assembly_1__model_1

2bnd__assembly_1__model_1 | I(q)

2bnd__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

The structure of E. coli UMP kinase in complex with UDP

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

2bnd__assembly_1__model_1

2bnd__assembly_1__model_1 | I(q)

2bnd__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)