9KMD | pdb_00009kmd

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

PDB DOI: https://doi.org/10.2210/pdb9KMD/pdb
EM Map EMD-62428: EMDB EMDataResource

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

Deposited: 2024-11-15 Released: 2025-11-26
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: 2.99 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

Nanomer Msp1 from S.cerevisiae (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: 337.59 kDa
Atom Count: 21,572
Modeled Residue Count: 2,702
Deposited Residue Count: 2,990
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, B, C, D, E A, B, C, D, E, F, G, H, I	330	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	J	20	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 AA [auth I] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain S [auth E] SDF format, chain U [auth F] SDF format, chain W [auth G] SDF format, chain Y [auth H] MOL2 format, chain AA [auth I] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E] MOL2 format, chain U [auth F] MOL2 format, chain W [auth G] MOL2 format, chain Y [auth H] mmCIF format, chain AA [auth I] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth E] mmCIF format, chain U [auth F] mmCIF format, chain W [auth G] mmCIF format, chain Y [auth H]	AA [auth I] K [auth A] M [auth B] O [auth C] Q [auth D] AA [auth I], K [auth A], M [auth B], O [auth C], Q [auth D], S [auth E], U [auth F], W [auth G], Y [auth H]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain AA [auth I] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H] Interactions & Density Focus chain AA [auth I] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth I] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain T [auth E] SDF format, chain V [auth F] SDF format, chain X [auth G] SDF format, chain Z [auth H] MOL2 format, chain BA [auth I] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] MOL2 format, chain V [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Z [auth H] mmCIF format, chain BA [auth I] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E] mmCIF format, chain V [auth F] mmCIF format, chain X [auth G] mmCIF format, chain Z [auth H]	BA [auth I] L [auth A] N [auth B] P [auth C] R [auth D] BA [auth I], L [auth A], N [auth B], P [auth C], R [auth D], T [auth E], V [auth F], X [auth G], Z [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth I] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H] Interactions & Density Focus chain BA [auth I] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H]