SAXSdb — 4m28

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

UDP-glucose pyrophosphorylase

Leishmania major

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine × 1 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4QDU3_LEIMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–494； UniProt 1–494

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	4m28
Deposition date deposition_date	2013-08-05
Structure title title	UDP-Glucose Pyrophosphorylase from Leishmania major in complex with UTP analog dUpCpp
Keywords keywords	UDP-glucose pyrophosphorylase, nucleotidyltransferase, Rossmann-like alpha/beta/alpha sandwich fold, transferase; 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.

4m28__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4m28__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4m28__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	31.74 Å
Rg (electron density)	31.02 Å
Total Rg	31.64 Å
Atom count	7516
Residues	966
Excluded volume	133820 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4m28__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4m28__assembly_2__model_1`	dimeric （2）	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	UDP-glucose pyrophosphorylase
Molecular weight formula_weight	56054.8 kDa
EC 编号 ec_number	2.7.7.9
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	3834

MENDMKSLSAAAQACVKKMRDAKVNEACIRTFIAQHVMVSKGETGSIPDSAIMPVDSLDALDSLTIECDNAVLQSTVVLKLNGGLGTGMGLCDAKTLLEVKDGKTFLDFTALQVQYLRQHCSEHLRFMLMDSFNTSASTKSFLKARYPWLYQVFDSEVELMQNQVPKILQDTLEPAAWAENPAYEWAPPGHGDIYTALYGSGKLQELVEQGYRYMFVSNGDNLGATIDKRVLAYMEKEKIDFLMEVCRRTESDKKGGHLARQTVYVKGKDGQPDAEKRVLLLRESAQCPKADMESFQDINKYSFFNTNNLWIRLPVLLETMQEHGGTLPLPVIRNEKTVDSSNSASPKVYQLETAMGAAIAMFESASAIVVPRSRFAPVKTCADLLALRSDAYVVTDDFRLVLDDRCHGHPPVVDLDSAHYKMMNGFEKLVQHGVPSLVECKRVTVKGLVQFGAGNVLTGTVTIENTDSASAFVIPDGAKLNDTTASPQQSTNKMRPLEHHHHHH

Source Source

Source organism organism	Leishmania major
NCBI taxonomy ID ncbi_taxonomy_id	5664
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine
Molecular weight formula_weight	466.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	76

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4m28A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	4m28A02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

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Unit-cell length a length_a	72.250 Å
Unit-cell length b length_b	108.470 Å
Unit-cell length c length_c	152.590 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	47.270 Å
R factor r_factor	0.2164
R_work r_work	0.2133
R_free r_free	0.2791

UDP-Glucose Pyrophosphorylase from Leishmania major in complex with UTP analog dUpCpp

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

UDP-glucose pyrophosphorylase

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

4m28__assembly_2__model_1

4m28__assembly_2__model_1 | I(q)

4m28__assembly_2__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

UDP-Glucose Pyrophosphorylase from Leishmania major in complex with UTP analog dUpCpp

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

UDP-glucose pyrophosphorylase

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

4m28__assembly_2__model_1

4m28__assembly_2__model_1 | I(q)

4m28__assembly_2__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)