9L6W | pdb_00009l6w

Hexamer Msp1 from S.cerevisiae(with a catalytic dead mutation) in complex with an unknown peptide substrate

PDB DOI: https://doi.org/10.2210/pdb9L6W/pdb
EM Map EMD-62865: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Saccharomyces cerevisiae S288C, Escherichia coli BL21(DE3)
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-12-25 Released: 2025-12-31
Deposition Author(s): Chengdong, H., Simin, W., Xuan, C.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.07 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Hexamer Msp1 from S.cerevisiaec(with a catalytic dead mutation) in complex with an unknown peptide substrate

Chengdong, H., Simin, W., Xuan, C.

To be published.

Macromolecule Content

Total Structure Weight: 246.57 kDa
Atom Count: 14,079
Modeled Residue Count: 1,759
Deposited Residue Count: 2,184
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer mitochondrial transmembrane helix translocase	A [auth B] B [auth F] C [auth E] D E [auth C] A [auth B], B [auth F], C [auth E], D, E [auth C], F [auth A]	362	Saccharomyces cerevisiae S288C	Mutation(s): 1 Gene Names: MSP1, YTA4, YGR028W EC: 7.4.2
UniProt
Find proteins for P28737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P28737 Go to UniProtKB: P28737
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28737
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
An unknown peptide substrate	G	12	Escherichia coli BL21(DE3)	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth F] SDF format, chain L [auth E] SDF format, chain N [auth D] SDF format, chain P [auth C] SDF format, chain R [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth F] MOL2 format, chain L [auth E] MOL2 format, chain N [auth D] MOL2 format, chain P [auth C] MOL2 format, chain R [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth F] mmCIF format, chain L [auth E] mmCIF format, chain N [auth D] mmCIF format, chain P [auth C] mmCIF format, chain R [auth A]	H [auth B] J [auth F] L [auth E] N [auth D] P [auth C] H [auth B], J [auth F], L [auth E], N [auth D], P [auth C], R [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain H [auth B] Focus chain J [auth F] Focus chain L [auth E] Focus chain N [auth D] Focus chain P [auth C] Focus chain R [auth A] Interactions & Density Focus chain H [auth B] Focus chain J [auth F] Focus chain L [auth E] Focus chain N [auth D] Focus chain P [auth C] Focus chain R [auth A]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain K [auth F] SDF format, chain M [auth E] SDF format, chain O [auth D] SDF format, chain Q [auth C] SDF format, chain S [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth F] MOL2 format, chain M [auth E] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth F] mmCIF format, chain M [auth E] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth A]	I [auth B] K [auth F] M [auth E] O [auth D] Q [auth C] I [auth B], K [auth F], M [auth E], O [auth D], Q [auth C], S [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain K [auth F] Focus chain M [auth E] Focus chain O [auth D] Focus chain Q [auth C] Focus chain S [auth A] Interactions & Density Focus chain I [auth B] Focus chain K [auth F] Focus chain M [auth E] Focus chain O [auth D] Focus chain Q [auth C] Focus chain S [auth A]