SAXSdb — 9vp6

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

Glucose-6-phosphate 1-dehydrogenase

Leishmania donovani

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	6-O-phosphono-beta-D-glucopyranose × 2 GLYCEROL × 4 1,2-ETHANEDIOL × 8 DI(HYDROXYETHYL)ETHER × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A2CIK6_LEIDO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 35–596； UniProt 1–562 Author chain B； PDBConstruct 35–596； UniProt 1–562

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	9vp6
Deposition date deposition_date	2025-07-02
Last revision last_revision	2025-11-05
Structure title title	Glucose-6-phosphate dehydrogenase from Leishmania donovani in complex with substrate
Keywords keywords	Glucose-6-phosphate dehydrogenase, Rossmann fold, complex form, substrate, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

9vp6__assembly_1__model_1

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

Download this curve (.dat)

9vp6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9vp6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	49.58 Å
Rg (electron density)	49.71 Å
Total Rg	49.71 Å
Atom count	16376
Residues	2118
Excluded volume	291670 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9vp6__assembly_1__model_1`	tetrameric （4）	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 (6)

Entity 1 Entity 1 polymer

Description description	Glucose-6-phosphate 1-dehydrogenase
Molecular weight formula_weight	66933.8 kDa
EC 编号 ec_number	1.1.1.49
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	8761

MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSEEQSHADQDAYVADVDGILDVLRAQVLERKPDDIFQFISKSALSLQKDRGAESCDRINCKVKDEQKSRALTIIVFGASGDLAKKKTFPALFDLYCGGLLPPEVNIIGYARTKVDDVEKWKHETLMKYFSNLSERGCHAEDFLKHISYFCGAYDSVDDFKRLDAVIREKENAFKGPEKGGNRLFYLALPPSVFASVCESIHKGAMPQEVGGWVRVIIEKPFGRDTKSSAELSQALEPFFDESQLYRIDHYLGKEMVQNIITTRFANRIFSAVWNASNIACVQITFKETIGTEGRGGYFDSIGIIRDVMQNHLTQILALLAMEKPRSLDAECIRDEKVSVLKCIEPITKENCVLGQYTASADGSIPGYLEDVTVPEGSTCPTFAVMRLNINNDRWAGVPFILKAGKAVEQKYVAIRIQFRDEVHPYGEATQRNELVIRAQPSEAMYVKITTKVPGLSGDLRQTHQTELDLTYHTRYDVRLPDAYESLINDALLGNSTNFVRKDELDVAWRIFTPLLHQIDSGEIKPIPYQAGTRGPKEADEFIANNGFKHQKGYHWLPSNKL

Source Source

Source organism organism	Leishmania donovani
NCBI taxonomy ID ncbi_taxonomy_id	5661
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	6-O-phosphono-beta-D-glucopyranose
Molecular weight formula_weight	260.1 kDa
Source method src_method	syn
Copy count entity_count	1

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	2

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	573

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Unit-cell length a length_a	193.396 Å
Unit-cell length b length_b	92.381 Å
Unit-cell length c length_c	70.628 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.44 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	29.554 Å
R factor r_factor	—
R_work r_work	0.2278
R_free r_free	0.3142

Glucose-6-phosphate dehydrogenase from Leishmania donovani in complex with substrate

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

Glucose-6-phosphate 1-dehydrogenase

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

9vp6__assembly_1__model_1

9vp6__assembly_1__model_1 | I(q)

9vp6__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 (6)

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 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Glucose-6-phosphate dehydrogenase from Leishmania donovani in complex with substrate

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

Glucose-6-phosphate 1-dehydrogenase

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

9vp6__assembly_1__model_1

9vp6__assembly_1__model_1 | I(q)

9vp6__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 (6)

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 non-polymer

Entity 6 Entity 6 water

7. Citations (1)