SAXSdb — 9gng

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

Isoform Mt-VDAC1 of Non-selective voltage-gated ion channel VDAC1

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(4S)-2-METHYL-2,4-PENTANEDIOL × 1 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VDAC1_MOUSE
Isoform	Q60932-2
PDB entities	1
Chains and sequence ranges	Author chain X； PDBConstruct 13–295； UniProt 1–283

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	9gng
Deposition date deposition_date	2024-09-03
Structure title title	mouse VDAC1 in complex with MPD
Keywords keywords	ion channel, VA binding site, NADH, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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.

9gng__assembly_1__model_1

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

Download this curve (.dat)

9gng__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9gng__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.97 Å
Rg (electron density)	21.24 Å
Total Rg	22.14 Å
Atom count	2197
Residues	283
Excluded volume	39067 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9gng__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 (4)

Entity 1 Entity 1 polymer

Description description	Isoform Mt-VDAC1 of Non-selective voltage-gated ion channel VDAC1
Molecular weight formula_weight	32195.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X
Atom count atom_count	2269

MRGSHHHHHHGSMAVPPTYADLGKSARDVFTKGYGFGLIKLDLKTKSENGLEFTSSGSANTETTKVNGSLETKYRWTEYGLTFTEKWNTDNTLGTEITVEDQLARGLKLTFDSSFSPNTGKKNAKIKTGYKREHINLGCDVDFDIAGPSIRGALVLGYEGWLAGYQMNFETSKSRVTQSNFAVGYKTDEFQLHTNVNDGTEFGGSIYQKVNKKLETAVNLAWTAGNSNTRFGIAAKYQVDPDACFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKNVNAGGHKLGLGLEFQA

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Molecular weight formula_weight	678.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	49

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Unit-cell length a length_a	99.426 Å
Unit-cell length b length_b	58.354 Å
Unit-cell length c length_c	66.822 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.17 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	66.140 Å
R factor r_factor	0.2452
R_work r_work	0.2429
R_free r_free	0.2985

mouse VDAC1 in complex with MPD

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

Isoform Mt-VDAC1 of Non-selective voltage-gated ion channel VDAC1

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

9gng__assembly_1__model_1

9gng__assembly_1__model_1 | I(q)

9gng__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 (4)

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 water

7. Citations (1)

mouse VDAC1 in complex with MPD

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

Isoform Mt-VDAC1 of Non-selective voltage-gated ion channel VDAC1

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

9gng__assembly_1__model_1

9gng__assembly_1__model_1 | I(q)

9gng__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 (4)

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 water

7. Citations (1)