9GNG

mouse VDAC1 in complex with MPD

PDB DOI: https://doi.org/10.2210/pdb9GNG/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-03 Released: 2025-01-08
Deposition Author(s): Lolicato, M., Arrigoni, C.
Funding Organization(s): Italian Ministry of Education

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.298
R-Value Work: 0.243
R-Value Observed: 0.245

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Protocol for high-yield bacterial expression and purification of the voltage-dependent anion chan- nel 1 for high-throughput biophysical assays

Lolicato, M., Arrigoni, C.

(2024) Star Protocols

DOI: https://doi.org/10.1016/j.xpro.2024.103557

Macromolecule Content

Total Structure Weight: 32.99 kDa
Atom Count: 2,269
Modelled Residue Count: 283
Deposited Residue Count: 295
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform Mt-VDAC1 of Non-selective voltage-gated ion channel VDAC1	A [auth X]	295	Mus musculus	Mutation(s): 0 Gene Names: Vdac1, Vdac5
UniProt & NIH Common Fund Data Resources
Find proteins for Q60932 (Mus musculus) Explore Q60932 Go to UniProtKB: Q60932
IMPC: MGI:106919
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q60932
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PX4 Query on PX4 Download Ideal Coordinates CCD File SDF format, chain C [auth X] MOL2 format, chain C [auth X] mmCIF format, chain C [auth X]	C [auth X]	1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₃₆ H₇₃ N O₈ P CITHEXJVPOWHKC-UUWRZZSWSA-O		Interactions Focus chain C [auth X] Interactions & Density Focus chain C [auth X]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.298
R-Value Work: 0.243
R-Value Observed: 0.245
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.426	α = 90
b = 58.354	β = 98.17
c = 66.822	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
Aimless	data scaling
Coot	model building
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Italian Ministry of Education	Italy	--

Revision History (Full details and data files)

Version 1.0: 2025-01-08
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.