SMTL ID : 7xbz.1

Crystal structure of Staphylococcus aureus ClpP in complex with R-ZG197

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-14-mer

Ligands

12 x D4E: (6S,9aS)-6-[(2S)-butan-2-yl]-8-[(1R)-1-naphthalen-1-ylethyl]-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide(Non-covalent)

D4E.1: 16 residues within 4Å: Chain A: V.45, L.49, F.50, Q.52, A.53, H.83 Chain B: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Ligands: MPD.7 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.29, B:I.29, B:Y.61, B:Y.61, B:Y.63, B:I.91, B:I.93, A:V.45, A:L.49, A:L.49, A:A.53 Halogen bonds: B:R.23 Hydrogen bonds: A:Q.52 D4E.8: 16 residues within 4Å: Chain C: V.45, L.49, F.50, Q.52, A.53, T.80, H.83 Chain D: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 17 PLIP interactions: 10 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:D.27, D:I.29, D:I.29, D:Y.61, D:Y.61, D:Y.63, D:Y.63, D:I.91, D:I.93, C:V.45, C:L.49, C:L.49, C:L.49, C:A.53, C:T.80 Halogen bonds: D:R.23, C:F.50 D4E.12: 16 residues within 4Å: Chain D: V.45, L.49, F.50, Q.52, A.53, T.80, H.83 Chain E: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 14 PLIP interactions: 7 interactions with chain D, 7 interactions with chain E Hydrophobic interactions: D:V.45, D:L.49, D:L.49, D:L.49, D:A.53, D:T.80, E:D.27, E:I.29, E:Y.63, E:I.91, E:I.91, E:I.93 Hydrogen bonds: D:Q.52 Halogen bonds: E:R.23 D4E.13: 16 residues within 4Å: Chain E: V.45, L.49, F.50, Q.52, A.53, T.80, H.83 Chain F: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 13 PLIP interactions: 5 interactions with chain E, 8 interactions with chain F Hydrophobic interactions: E:V.45, E:L.49, E:L.49, E:A.53, E:T.80, F:D.27, F:I.29, F:I.29, F:Y.61, F:Y.61, F:Y.63, F:I.93 Halogen bonds: F:R.23 D4E.17: 16 residues within 4Å: Chain A: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Chain G: V.45, L.49, F.50, Q.52, A.53, T.80, H.83 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain G Hydrophobic interactions: A:D.27, A:I.29, A:I.29, A:Y.61, A:Y.61, A:Y.63, A:I.91, A:I.93, G:V.45, G:L.49, G:L.49, G:L.49, G:A.53, G:T.80 D4E.22: 16 residues within 4Å: Chain H: V.45, L.49, F.50, Q.52, A.53, T.80, H.83 Chain I: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 16 PLIP interactions: 9 interactions with chain I, 7 interactions with chain H Hydrophobic interactions: I:D.27, I:I.29, I:I.29, I:Y.61, I:Y.61, I:Y.63, I:I.91, I:I.93, H:V.45, H:L.49, H:L.49, H:L.49, H:A.53, H:T.80 Halogen bonds: I:R.23 Water bridges: H:Q.52 D4E.23: 15 residues within 4Å: Chain I: V.45, L.49, F.50, Q.52, A.53, H.83 Chain J: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 15 PLIP interactions: 10 interactions with chain J, 5 interactions with chain I Hydrophobic interactions: J:D.27, J:I.29, J:I.29, J:Y.61, J:Y.61, J:Y.63, J:Y.63, J:I.91, J:I.93, I:V.45, I:L.49, I:L.49, I:L.49, I:A.53 Halogen bonds: J:R.23 D4E.28: 16 residues within 4Å: Chain J: V.45, L.49, F.50, Q.52, A.53, T.80, H.83 Chain K: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 11 PLIP interactions: 6 interactions with chain K, 5 interactions with chain J Hydrophobic interactions: K:I.29, K:I.29, K:Y.63, K:I.91, K:I.91, K:I.93, J:V.45, J:L.49, J:L.49, J:A.53, J:T.80 D4E.31: 14 residues within 4Å: Chain K: V.45, F.50, Q.52, A.53, T.80, H.83 Chain L: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93 10 PLIP interactions: 7 interactions with chain L, 3 interactions with chain K Hydrophobic interactions: L:D.27, L:I.29, L:I.29, L:Y.61, L:Y.63, L:I.93, K:V.45, K:A.53, K:T.80 Halogen bonds: L:R.23 D4E.33: 17 residues within 4Å: Chain L: V.45, L.49, F.50, Q.52, A.53, T.80, H.83, I.84 Chain M: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 16 PLIP interactions: 8 interactions with chain L, 8 interactions with chain M Hydrophobic interactions: L:V.45, L:L.49, L:L.49, L:L.49, L:A.53, L:T.80, L:I.84, M:D.27, M:I.29, M:I.29, M:Y.61, M:Y.63, M:Y.63, M:I.93 Halogen bonds: L:F.50, M:R.23 D4E.36: 17 residues within 4Å: Chain H: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Chain N: V.45, L.49, F.50, Q.52, A.53, T.80, H.83, I.84 16 PLIP interactions: 9 interactions with chain H, 7 interactions with chain N Hydrophobic interactions: H:D.27, H:I.29, H:I.29, H:Y.61, H:Y.61, H:Y.63, H:I.91, H:I.93, N:V.45, N:L.49, N:L.49, N:L.49, N:A.53, N:T.80, N:I.84 Halogen bonds: H:R.23 D4E.37: 16 residues within 4Å: Chain M: V.45, L.49, F.50, Q.52, A.53, T.80, H.83 Chain N: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 14 PLIP interactions: 5 interactions with chain M, 9 interactions with chain N Hydrophobic interactions: M:V.45, M:L.49, M:L.49, M:A.53, M:T.80, N:D.27, N:I.29, N:I.29, N:Y.61, N:Y.61, N:Y.63, N:I.91, N:I.93 Halogen bonds: N:R.23

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: I.81, I.84, P.86 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:I.81, A:P.86, H2O.2, H2O.2 MG.3: 3 residues within 4Å: Chain A: N.173, F.174, L.175 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:F.174 MG.5: 3 residues within 4Å: Chain B: I.81, I.84, P.86 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:I.81, B:P.86, H2O.3, H2O.4 MG.9: 3 residues within 4Å: Chain C: I.81, I.84, P.86 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:I.81, C:P.86, H2O.6 MG.15: 3 residues within 4Å: Chain F: I.81, I.84, P.86 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:I.81, F:P.86, H2O.9, H2O.9 MG.18: 3 residues within 4Å: Chain G: I.81, I.84, P.86 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:I.81, G:P.86, H2O.9, H2O.10 MG.20: 3 residues within 4Å: Chain H: I.81, I.84, P.86 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:I.81, H:P.86, H2O.11, H2O.12 MG.24: 3 residues within 4Å: Chain I: I.81, I.84, P.86 4 PLIP interactions: 2 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:I.81, I:P.86, H2O.14, H2O.15 MG.26: 3 residues within 4Å: Chain J: I.81, I.84, P.86 4 PLIP interactions: 2 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:I.81, J:P.86, H2O.16, H2O.16 MG.29: 4 residues within 4Å: Chain K: I.81, I.84, P.86, V.88 3 PLIP interactions: 2 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:I.81, K:P.86, H2O.17 MG.34: 4 residues within 4Å: Chain M: I.81, I.84, P.86, V.88 3 PLIP interactions: 2 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:I.81, M:P.86, H2O.18 MG.38: 3 residues within 4Å: Chain N: I.81, I.84, P.86 3 PLIP interactions: 2 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:I.81, N:P.86, H2O.19

15 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 9 residues within 4Å: Chain A: V.71, S.98, M.99, S.101, F.102, I.122, H.123, Q.124, L.150 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.71, A:F.102, A:L.150 Hydrogen bonds: A:H.123, A:H.123 MPD.6: 9 residues within 4Å: Chain B: S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154, T.169 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.102, B:I.122, B:L.150, B:L.154, B:T.169 Hydrogen bonds: B:H.123, B:H.123 MPD.7: 6 residues within 4Å: Chain A: F.50, A.53, Q.54 Chain B: E.9, R.23 Ligands: D4E.1 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.50, A:A.53 Hydrogen bonds: B:R.23 MPD.10: 9 residues within 4Å: Chain C: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.71, C:F.102, C:L.150, C:L.154 Hydrogen bonds: C:H.123, C:H.123 MPD.11: 8 residues within 4Å: Chain D: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.71, D:F.102, D:L.150 Hydrogen bonds: D:H.123, D:H.123 MPD.14: 9 residues within 4Å: Chain E: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:V.71, E:F.102, E:L.150, E:L.154 Hydrogen bonds: E:H.123, E:H.123 Water bridges: E:M.99 MPD.16: 9 residues within 4Å: Chain F: S.98, M.99, S.101, F.102, I.122, H.123, Q.124, L.150, L.154 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:F.102, F:L.150, F:L.154 Hydrogen bonds: F:H.123, F:H.123 MPD.19: 11 residues within 4Å: Chain G: S.98, M.99, S.101, F.102, I.122, H.123, Q.124, P.125, L.150, L.154, T.169 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:F.102, G:L.150, G:L.154, G:T.169 Hydrogen bonds: G:H.123 Water bridges: G:S.98, G:M.99 MPD.21: 8 residues within 4Å: Chain H: S.98, M.99, S.101, F.102, I.122, H.123, P.125, L.150 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:F.102, H:P.125, H:L.150 Hydrogen bonds: H:S.98, H:H.123 MPD.25: 10 residues within 4Å: Chain I: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154, T.169 8 PLIP interactions: 8 interactions with chain I Hydrophobic interactions: I:V.71, I:F.102, I:I.122, I:L.150, I:L.154, I:T.169 Hydrogen bonds: I:H.123, I:H.123 MPD.27: 9 residues within 4Å: Chain J: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:V.71, J:F.102, J:L.150, J:L.154 Hydrogen bonds: J:H.123, J:H.123 MPD.30: 7 residues within 4Å: Chain K: S.98, M.99, S.101, I.122, H.123, Q.124, L.154 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:I.122, K:L.154 Hydrogen bonds: K:H.123, K:H.123 MPD.32: 9 residues within 4Å: Chain L: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 6 PLIP interactions: 6 interactions with chain L Hydrophobic interactions: L:V.71, L:F.102, L:L.150, L:L.154 Hydrogen bonds: L:H.123, L:H.123 MPD.35: 8 residues within 4Å: Chain M: S.98, M.99, S.101, F.102, I.122, H.123, P.125, L.150 5 PLIP interactions: 5 interactions with chain M Hydrophobic interactions: M:F.102, M:P.125, M:L.150 Hydrogen bonds: M:H.123, M:H.123 MPD.39: 9 residues within 4Å: Chain N: S.98, M.99, S.101, F.102, I.122, H.123, P.125, L.150, T.169 7 PLIP interactions: 7 interactions with chain N Hydrophobic interactions: N:F.102, N:P.125, N:L.150, N:T.169 Hydrogen bonds: N:S.98, N:H.123 Water bridges: N:M.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wei, B. et al., Anti-infective therapy using species-specific activators of Staphylococcus aureus ClpP. Nat Commun (2022)

Release Date

2022-11-16

Peptides

ATP-dependent Clp protease proteolytic subunit: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

ATP-dependent Clp protease proteolytic subunit

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