SMTL ID : 9irm.1

Structure of ClpP from Staphylococcus aureus in complex with ZG283

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-14-mer

Ligands

14 x WBW: (6S,9aS)-8-(anthracen-9-ylmethyl)-6-[(2S)-butan-2-yl]-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)

WBW.1: 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 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain G Hydrophobic interactions: A:D.27, A:I.29, A:I.29, A:Y.61, A:Y.63, A:Y.63, A:I.91, A:I.91, A:I.93, G:V.45, G:L.49, G:L.49, G:A.53, G:T.80 Water bridges: A:D.27, A:D.27 Halogen bonds: A:R.23 WBW.3: 17 residues within 4Å: Chain A: V.45, L.49, F.50, Q.52, A.53, T.80, H.83 Chain B: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Ligands: MPD.5 16 PLIP interactions: 11 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:D.27, B:I.29, B:Y.61, B:Y.63, B:Y.63, B:I.91, B:I.91, B:I.93, A:V.45, A:L.49, A:L.49, A:A.53, A:T.80 Water bridges: B:D.27, B:D.27 Halogen bonds: B:R.23 WBW.6: 15 residues within 4Å: Chain B: L.49, F.50, Q.52, A.53, T.80, H.83 Chain C: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 17 PLIP interactions: 6 interactions with chain B, 11 interactions with chain C Hydrophobic interactions: B:L.49, B:L.49, B:A.53, B:T.80, C:I.29, C:I.29, C:Y.61, C:Y.63, C:Y.63, C:I.91, C:I.91, C:I.93 Hydrogen bonds: B:Q.52, C:Y.61 pi-Stacking: B:H.83 Water bridges: C:D.27 Halogen bonds: C:R.23 WBW.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.63, D:Y.63, D:I.91, D:I.91, D:I.93, C:V.45, C:L.49, C:L.49, C:A.53, C:T.80 Halogen bonds: D:R.23, C:L.49 pi-Stacking: C:H.83 WBW.10: 14 residues within 4Å: Chain D: L.49, F.50, 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 15 PLIP interactions: 9 interactions with chain E, 6 interactions with chain D Hydrophobic interactions: E:I.29, E:I.29, E:Y.61, E:Y.63, E:Y.63, E:I.91, E:I.91, E:I.93, D:L.49, D:L.49, D:A.53, D:T.80 Halogen bonds: E:R.23 Hydrogen bonds: D:Q.52 pi-Stacking: D:H.83 WBW.11: 14 residues within 4Å: Chain E: L.49, F.50, 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: 9 interactions with chain F, 4 interactions with chain E Hydrophobic interactions: F:I.29, F:I.29, F:Y.61, F:Y.63, F:Y.63, F:I.91, F:I.91, F:I.93, E:L.49, E:L.49, E:A.53 Halogen bonds: F:R.23, E:L.49 WBW.14: 14 residues within 4Å: Chain F: L.49, F.50, A.53, T.80, H.83 Chain G: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 15 PLIP interactions: 9 interactions with chain G, 6 interactions with chain F Hydrophobic interactions: G:I.29, G:I.29, G:Y.61, G:Y.63, G:Y.63, G:I.91, G:I.91, G:I.93, F:L.49, F:L.49, F:A.53, F:T.80 Halogen bonds: G:R.23, F:L.49 Hydrogen bonds: F:Q.52 WBW.16: 17 residues within 4Å: Chain H: R.23, L.24, D.27, I.29, M.31, 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 17 PLIP interactions: 11 interactions with chain H, 6 interactions with chain N Hydrophobic interactions: H:D.27, H:I.29, H:Y.61, H:Y.63, H:Y.63, H:I.91, H:I.91, H:I.93, N:V.45, N:L.49, N:L.49, N:A.53, N:T.80, N:H.83 Water bridges: H:D.27, H:D.27 Halogen bonds: H:R.23 WBW.18: 17 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 Ligands: MPD.20 19 PLIP interactions: 12 interactions with chain I, 7 interactions with chain H Hydrophobic interactions: I:D.27, I:I.29, I:Y.61, I:Y.63, I:Y.63, I:I.91, I:I.91, I:I.93, H:V.45, H:L.49, H:L.49, H:A.53, H:T.80, H:H.83 Water bridges: I:D.27, I:D.27, I:Y.61 Halogen bonds: I:R.23 pi-Stacking: H:H.83 WBW.21: 17 residues within 4Å: Chain I: V.45, L.49, F.50, Q.52, A.53, T.80, H.83 Chain J: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, L.115, M.190 18 PLIP interactions: 8 interactions with chain I, 10 interactions with chain J Hydrophobic interactions: I:V.45, I:L.49, I:L.49, I:A.53, I:T.80, I:H.83, J:D.27, J:I.29, J:Y.61, J:Y.63, J:Y.63, J:I.91, J:I.91, J:I.93, J:L.115 Hydrogen bonds: I:Q.52 pi-Stacking: I:H.83 Halogen bonds: J:R.23 WBW.23: 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 16 PLIP interactions: 10 interactions with chain K, 6 interactions with chain J Hydrophobic interactions: K:D.27, K:I.29, K:I.29, K:Y.61, K:Y.63, 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 Halogen bonds: K:R.23, J:L.49 WBW.25: 17 residues within 4Å: Chain K: V.45, L.49, F.50, Q.52, A.53, T.80, H.83 Chain L: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 13 PLIP interactions: 9 interactions with chain L, 4 interactions with chain K Hydrophobic interactions: L:L.24, L:I.29, L:I.29, L:Y.61, L:Y.63, L:Y.63, L:I.91, L:I.93, K:L.49, K:L.49, K:A.53 Halogen bonds: L:R.23 Hydrogen bonds: K:Q.52 WBW.27: 16 residues within 4Å: Chain L: V.45, L.49, F.50, Q.52, A.53, T.80, H.83 Chain M: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 10 PLIP interactions: 6 interactions with chain M, 4 interactions with chain L Hydrophobic interactions: M:I.29, M:Y.61, M:Y.63, M:Y.63, M:I.93, L:V.45, L:L.49, L:L.49, L:A.53 Halogen bonds: M:R.23 WBW.29: 17 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, M.31, Y.61, Y.63, I.91, I.93, M.190 16 PLIP interactions: 6 interactions with chain M, 10 interactions with chain N Hydrophobic interactions: M:V.45, M:L.49, M:L.49, M:L.49, M:A.53, M:T.80, N:I.29, N:Y.61, N:Y.63, N:Y.63, N:I.91, N:I.91, N:I.93 Water bridges: N:D.27, N:D.27 Halogen bonds: N:R.23

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

MPD.2: 6 residues within 4Å: Chain A: S.98, M.99, S.101, I.122, H.123, L.150 Ligand excluded by PLIP MPD.4: 9 residues within 4Å: Chain B: S.98, M.99, S.101, F.102, I.122, H.123, Q.124, L.150, L.154 Ligand excluded by PLIP MPD.5: 5 residues within 4Å: Chain A: F.50, A.53, Q.54 Chain B: R.23 Ligands: WBW.3 Ligand excluded by PLIP MPD.7: 7 residues within 4Å: Chain C: S.98, M.99, S.101, I.122, H.123, L.150, L.154 Ligand excluded by PLIP MPD.9: 7 residues within 4Å: Chain D: S.98, M.99, S.101, I.122, H.123, L.150, L.154 Ligand excluded by PLIP MPD.12: 7 residues within 4Å: Chain E: S.98, M.99, S.101, I.122, H.123, L.150, L.154 Ligand excluded by PLIP MPD.13: 9 residues within 4Å: Chain F: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 Ligand excluded by PLIP MPD.15: 7 residues within 4Å: Chain G: V.71, S.98, M.99, I.122, H.123, L.150, L.154 Ligand excluded by PLIP MPD.17: 7 residues within 4Å: Chain H: S.98, M.99, S.101, F.102, I.122, H.123, L.150 Ligand excluded by PLIP MPD.19: 9 residues within 4Å: Chain I: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 Ligand excluded by PLIP MPD.20: 6 residues within 4Å: Chain H: F.50, A.53, Q.54 Chain I: E.9, R.23 Ligands: WBW.18 Ligand excluded by PLIP MPD.22: 9 residues within 4Å: Chain J: V.71, S.98, M.99, F.102, I.122, H.123, Q.124, L.150, L.154 Ligand excluded by PLIP MPD.24: 8 residues within 4Å: Chain K: V.71, S.98, M.99, S.101, I.122, H.123, L.150, L.154 Ligand excluded by PLIP MPD.26: 7 residues within 4Å: Chain L: S.98, M.99, S.101, I.122, H.123, L.150, L.154 Ligand excluded by PLIP MPD.28: 9 residues within 4Å: Chain M: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 Ligand excluded by PLIP MPD.30: 6 residues within 4Å: Chain N: S.98, M.99, S.101, I.122, H.123, L.150 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, T. et al., Structure-guided development of selective caseinolytic protease P agonists as antistaphylococcal agents. Cell Rep Med (2024)

Release Date

2024-10-23

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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