SMTL ID : 9b70.1

Cryo-EM structure of MraY in complex with analogue 2

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-2-[[3-[[[(2~{S})-6-azanyl-2-(hexadecanoylamino)hexanoyl]amino]methyl]phenyl]methylamino]-3-[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]propanoic acid

01.1: 25 residues within 4Å: Chain A: K.76, T.81, G.133, I.136, F.140, G.190, 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, S.274, V.302, T.305, I.309, H.331 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.197, A:L.197, A:V.302, A:T.305 Hydrogen bonds: A:K.76, A:T.81, A:N.196, A:D.199, A:D.199, A:D.202, A:N.261, A:M.269, A:G.270, A:S.274 Water bridges: A:G.203 pi-Stacking: A:F.268 01.2: 25 residues within 4Å: Chain D: K.76, T.81, G.133, I.136, F.140, G.190, 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, S.274, V.302, T.305, I.309, H.331 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:L.197, D:L.197, D:V.302, D:T.305 Hydrogen bonds: D:K.76, D:T.81, D:N.196, D:D.199, D:D.199, D:D.202, D:N.261, D:M.269, D:G.270, D:S.274 Water bridges: D:G.203 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

Phospho-N-acetylmuramoyl-pentapeptide-transferase: AD
MraYAA nanobody: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
A

B
G

C
H

Membrane

We predict this structure to be a membrane protein.
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Phospho-N-acetylmuramoyl-pentapeptide-transferase

MraYAA nanobody

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