SAXSdb — 4m2b

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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	URIDINE-5'-DIPHOSPHATE-GLUCOSE × 1 water × 1	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	4m2b
Deposition date deposition_date	2013-08-05
Structure title title	Crystal structure of L281D mutant of udp-glucose pyrophosphorylase from leishmania major in complex with udp-glc
Keywords keywords	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.

4m2b__assembly_1__model_1

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

Download this curve (.dat)

4m2b__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4m2b__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.10 Å
Rg (electron density)	23.06 Å
Total Rg	23.84 Å
Atom count	3766
Residues	483
Excluded volume	67007 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4m2b__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 (3)

Entity 1 Entity 1 polymer

Description description	UDP-glucose pyrophosphorylase
Molecular weight formula_weight	56056.7 kDa
EC 编号 ec_number	2.7.7.9
Mutation mutation	L281D
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	4159

MENDMKSLSAAAQACVKKMRDAKVNEACIRTFIAQHVMVSKGETGSIPDSAIMPVDSLDALDSLTIECDNAVLQSTVVLKLNGGLGTGMGLCDAKTLLEVKDGKTFLDFTALQVQYLRQHCSEHLRFMLMDSFNTSASTKSFLKARYPWLYQVFDSEVELMQNQVPKILQDTLEPAAWAENPAYEWAPPGHGDIYTALYGSGKLQELVEQGYRYMFVSNGDNLGATIDKRVLAYMEKEKIDFLMEVCRRTESDKKGGHLARQTVYVKGKDGQPDAEKRVLDLRESAQCPKADMESFQDINKYSFFNTNNLWIRLPVLLETMQEHGGTLPLPVIRNEKTVDSSNSASPKVYQLETAMGAAIAMFESASAIVVPRSRFAPVKTCADLLALRSDAYVVTDDFRLVLDDRCHGHPPVVDLDSAHYKMMNGFEKLVQHGVPSLVECKRVTVKGLVQFGAGNVLTGTVTIENTDSASAFVIPDGAKLNDTTASPQQSTNKMRPLEHHHHHH

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	URIDINE-5'-DIPHOSPHATE-GLUCOSE
Molecular weight formula_weight	566.3 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	393

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4m2bA01
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	4m2bA02
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	78.790 Å
Unit-cell length b length_b	86.900 Å
Unit-cell length c length_c	138.230 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	2.200 Å
Low-resolution limit resolution_low	23.400 Å
R factor r_factor	0.1780
R_work r_work	0.1750
R_free r_free	0.2420

Crystal structure of L281D mutant of udp-glucose pyrophosphorylase from leishmania major in complex with udp-glc

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

4m2b__assembly_1__model_1

4m2b__assembly_1__model_1 | I(q)

4m2b__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of L281D mutant of udp-glucose pyrophosphorylase from leishmania major in complex with udp-glc

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

4m2b__assembly_1__model_1

4m2b__assembly_1__model_1 | I(q)

4m2b__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)