SMTL ID : 9mhz.1

Cryo-EM structure of S. aureus TarGH in complex with Targocil-II and ATP-gamma-S in a catalytically incompetent conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x AV0: Lauryl Maltose Neopentyl Glycol(Non-covalent)

AV0.1: 15 residues within 4Å: Chain A: L.194, L.197, V.198, L.282, K.285, Y.286, Q.289, D.292, F.293 Chain B: K.12, E.13, R.15, A.27, T.77 Chain D: Y.58 17 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: A:L.194, A:L.197, A:L.197, A:L.197, A:V.198, A:L.282, B:A.27, D:Y.58 Hydrogen bonds: A:K.285, A:K.285, A:Y.286, A:Q.289, A:D.292, B:K.12, B:E.13, D:Y.58 Salt bridges: A:K.285 AV0.7: 15 residues within 4Å: Chain A: Y.58 Chain C: K.12, E.13, R.15, A.27, T.77 Chain D: L.194, L.197, V.198, L.282, K.285, Y.286, Q.289, D.292, F.293 17 PLIP interactions: 3 interactions with chain C, 12 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: C:A.27, D:L.194, D:L.197, D:L.197, D:L.197, D:V.198, D:L.282, A:Y.58 Hydrogen bonds: C:K.12, C:E.13, D:K.285, D:K.285, D:Y.286, D:Q.289, D:D.292, A:Y.58 Salt bridges: D:K.285

2 x 01: Targocil-II

01.2: 12 residues within 4Å: Chain A: I.83, R.84, Y.214, F.215, W.220, K.223, I.231 Chain D: M.77, V.78, L.81, G.82, I.83 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:R.84, A:F.215, A:W.220, A:W.220, A:W.220, A:I.231, D:L.81, D:I.83 Salt bridges: A:R.84, A:K.223 pi-Stacking: A:F.215, A:W.220, A:W.220 01.8: 12 residues within 4Å: Chain A: M.77, V.78, L.81, G.82, I.83 Chain D: I.83, R.84, Y.214, F.215, W.220, K.223, I.231 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:R.84, D:F.215, D:W.220, D:W.220, D:W.220, D:I.231, A:L.81, A:I.83 Salt bridges: D:R.84, D:K.223 pi-Stacking: D:F.215, D:W.220, D:W.220

2 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.3: 18 residues within 4Å: Chain B: Y.14, F.37, A.39, N.59, G.60, S.61, G.62, K.63, S.64, T.65, H.201, R.260 Chain C: F.136, K.143, S.145, G.147, M.148 Ligands: MG.4 16 PLIP interactions: 5 interactions with chain C, 11 interactions with chain B Hydrogen bonds: C:S.145, C:G.147, B:N.59, B:G.60, B:G.60, B:S.61, B:G.62, B:K.63, B:S.64, B:S.64, B:T.65, B:T.65 Water bridges: C:S.146, C:S.146, C:S.146 pi-Stacking: B:Y.14 AGS.5: 18 residues within 4Å: Chain B: F.136, K.143, S.145, G.147, M.148 Chain C: Y.14, F.37, A.39, N.59, G.60, S.61, G.62, K.63, S.64, T.65, H.201, R.260 Ligands: MG.6 16 PLIP interactions: 5 interactions with chain B, 11 interactions with chain C Hydrogen bonds: B:S.145, B:G.147, C:N.59, C:G.60, C:G.60, C:S.61, C:G.62, C:K.63, C:S.64, C:S.64, C:T.65, C:T.65 Water bridges: B:S.146, B:S.146, B:S.146 pi-Stacking: C:Y.14

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain B: S.64 Chain C: S.146 Ligands: AGS.3 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.64, H2O.1, H2O.1, H2O.1 MG.6: 3 residues within 4Å: Chain B: S.146 Chain C: S.64 Ligands: AGS.5 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:S.64, H2O.1, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, F.K.K. et al., Cryo-EM analyses unveil details of mechanism and targocil-II mediated inhibition of S. aureus WTA transporter TarGH. Nat Commun (2025)

Release Date

2025-04-23

Peptides

Transport permease protein: AD
Teichoic acids export ATP-binding protein TagH: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
C

B
B

C
D

Membrane

We predict this structure to be a membrane protein.
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Transport permease protein

Teichoic acids export ATP-binding protein TagH

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