SMTL ID : 8do0.1

Cryo-EM structure of the human Sec61 complex inhibited by mycolactone

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x Q6B: [(6~{S},7~{S},9~{Z},12~{R})-12-[(~{Z},2~{S},6~{R},7~{R},9~{R})-4,6-dimethyl-7,9-bis(oxidanyl)dec-4-en-2-yl]-7,9-dimethyl-2-oxidanylidene-1-oxacyclododec-9-en-6-yl] (2~{E},4~{E},6~{E},8~{E},10~{E},12~{S},13~{S},15~{S})-4,6,10-trimethyl-12,13,15-tris(oxidanyl)hexadeca-2,4,6,8,10-pentaenoate(Non-covalent)

Q6B.1: 28 residues within 4Å: Chain C: F.62, M.65, I.68, L.69, S.82, V.85, T.86, L.89, I.123, Q.127, V.130, Y.131, S.177, I.179, S.180, I.183, S.287, N.288, I.289, I.292, A.296, N.300, V.303, I.304, M.307, L.449, I.453, Q.456 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:F.62, C:I.68, C:V.85, C:V.85, C:T.86, C:L.89, C:I.123, C:Q.127, C:V.130, C:Y.131, C:I.179, C:I.183, C:I.289, C:I.292, C:I.292, C:I.292, C:I.304 Hydrogen bonds: C:S.177, C:S.180, C:N.288, C:N.288, C:N.300, C:Q.456

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Itskanov, S. et al., A common mechanism of Sec61 translocon inhibition by small molecules. Nat.Chem.Biol. (2023)

Release Date

2023-05-24

Peptides

Protein transport protein Sec61 subunit gamma: A
Protein transport protein Sec61 subunit beta: B
Protein transport protein Sec61 subunit alpha isoform 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
A

Membrane

We predict this structure to be a membrane protein.
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Protein transport protein Sec61 subunit gamma

Protein transport protein Sec61 subunit beta

Protein transport protein Sec61 subunit alpha isoform 1

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