SMTL ID : 8cxr.2 (3 other biounits)

Crystal structure of MraY bound to a sphaerimicin analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.65 Å

Oligo State

hetero-1-1-mer

Ligands

1 x P5L: (1S,4R,5S,6R,7S,9S,10S,11S,13S,14R)-9-[(2S,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]-14-(hexadecanoyloxy)-5,6,13-trihydroxy-8,16-dioxa-2,11-diazatricyclo[9.3.1.1~4,7~]hexadecane-10-carboxylic acid(Non-covalent)

P5L.1: 25 residues within 4Å: Chain B: T.81, K.139, F.140, F.186, V.189, G.190, N.193, N.196, L.197, D.199, G.200, L.201, D.202, G.203, N.261, A.265, F.268, M.269, G.270, D.271, S.274, V.308, I.309, H.331, E.340 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.189, B:N.193 Hydrogen bonds: B:D.199, B:D.202, B:D.202, B:N.261, B:G.270, B:D.271 Salt bridges: B:K.139, B:H.331 pi-Stacking: B:F.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakaya, T. et al., Synthesis of macrocyclic nucleoside antibacterials and their interactions with MraY. Nat Commun (2022)

Release Date

2023-03-29

Peptides

MraYAA nanobody: A
Phospho-N-acetylmuramoyl-pentapeptide-transferase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
C

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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