SMTL ID : 9b71.1

Cryo-EM structure of MraY in complex with analogue 3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x 01: (2~{S},3~{S})-3-[(2~{S},3~{R},4~{S},5~{R})-5-(aminomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]oxy-3-[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]-2-[[4-[[[(2~{S})-5-carbamimidamido-2-(hexadecanoylamino)pentanoyl]amino]methyl]phenyl]methylamino]propanoic acid

01.1: 26 residues within 4Å: Chain B: K.76, T.81, G.133, I.134, I.136, K.139, F.186, G.190, S.191, N.193, A.194, N.196, L.197, D.199, G.200, L.201, D.202, G.203, N.261, F.268, M.269, G.270, D.271, V.302, T.305, H.331 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.186, B:L.197, B:V.302, B:T.305 Hydrogen bonds: B:K.76, B:T.81, B:I.134, B:N.196, B:D.199, B:D.202, B:D.202, B:N.261, B:M.269, B:G.270, B:H.331 Water bridges: B:L.204 Salt bridges: B:D.123 pi-Stacking: B:F.268 01.2: 26 residues within 4Å: Chain D: K.76, T.81, G.133, I.134, I.136, K.139, F.186, G.190, S.191, N.193, A.194, N.196, L.197, D.199, G.200, L.201, D.202, G.203, N.261, F.268, M.269, G.270, D.271, V.302, T.305, H.331 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:F.186, D:L.197, D:V.302, D:T.305 Hydrogen bonds: D:K.76, D:T.81, D:I.134, D:N.196, D:D.199, D:D.202, D:D.202, D:N.261, D:M.269, D:G.270, D:H.331 Water bridges: D:L.204 Salt bridges: D:D.123 pi-Stacking: D:F.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamamoto, K. et al., Development of a natural product optimization strategy for inhibitors against MraY, a promising antibacterial target. Nat Commun (2024)

Release Date

2024-06-26

Peptides

MraYAA Nanobody: AC
Phospho-N-acetylmuramoyl-pentapeptide-transferase: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

C
G

B
A

D
B

Membrane

We predict this structure to be a membrane protein.
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MraYAA Nanobody

Phospho-N-acetylmuramoyl-pentapeptide-transferase

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