SAXSdb — 9t7u

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

Glyceraldehyde-3-phosphate dehydrogenase 1

Staphylococcus aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	ACETIC ACID × 9 COPPER (I) ION × 4 SODIUM ION × 5 TRIETHYLENE GLYCOL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G3P1_STAAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain AAA； PDBConstruct 1–336； UniProt 1–336 Author chain BBB； PDBConstruct 1–336； UniProt 1–336 Author chain CCC； PDBConstruct 1–336； UniProt 1–336 Author chain DDD； PDBConstruct 1–336； UniProt 1–336

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	9t7u
Deposition date deposition_date	2025-11-11
Structure title title	Glyceraldehyde-3-phosphate dehydrogenase A (GAPDH)
Keywords keywords	;Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), protein copper binding, copper toxicity, copper homeostasis, Staphylococcus aureus, 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.

9t7u__assembly_1__model_1

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

Download this curve (.dat)

9t7u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9t7u__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.62 Å
Rg (electron density)	31.87 Å
Total Rg	32.46 Å
Atom count	10164
Residues	1334
Excluded volume	180170 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9t7u__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	Glyceraldehyde-3-phosphate dehydrogenase 1
Molecular weight formula_weight	36320.8 kDa
EC 编号 ec_number	1.2.1.12
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AAA,BBB,CCC,DDD
Atom count atom_count	10795

MAVKVAINGFGRIGRLAFRRIQEVEGLEVVAVNDLTDDDMLAHLLKYDTMQGRFTGEVEVVDGGFRVNGKEVKSFSEPDASKLPWKDLNIDVVLECTGFYTDKDKAQAHIEAGAKKVLISAPATGDLKTIVFNTNHQELDGSETVVSGASCTTNSLAPVAKVLNDDFGLVEGLMTTIHAYTGDQNTQDAPHRKGDKRRARAAAENIIPNSTGAAKAIGKVIPEIDGKLDGGAQRVPVATGSLTELTVVLEKQDVTVEQVNEAMKNASNESFGYTEDEIVSSDVVGMTYGSLFDATQTRVMSVGDRQLVKVAAWYDNEMSYTAQLVRTLAYLAELSK

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 3 Entity 3 non-polymer

Description description	COPPER (I) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 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	631

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Unit-cell length a length_a	98.901 Å
Unit-cell length b length_b	98.901 Å
Unit-cell length c length_c	252.217 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	32

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	46.830 Å
R factor r_factor	—
R_work r_work	0.1524
R_free r_free	0.2094

Glyceraldehyde-3-phosphate dehydrogenase A (GAPDH)

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

Glyceraldehyde-3-phosphate dehydrogenase 1

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

9t7u__assembly_1__model_1

9t7u__assembly_1__model_1 | I(q)

9t7u__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)

Glyceraldehyde-3-phosphate dehydrogenase A (GAPDH)

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

Glyceraldehyde-3-phosphate dehydrogenase 1

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

9t7u__assembly_1__model_1

9t7u__assembly_1__model_1 | I(q)

9t7u__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)