SMTL ID : 9irp.1

Structure of ClpP from Staphylococcus aureus in complex with ZG297

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-14-mer

Ligands

14 x Z53: (6S,9aS)-6-[(2S)-butan-2-yl]-4,7-bis(oxidanylidene)-8-(phenanthren-9-ylmethyl)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide(Non-covalent)

Z53.1: 17 residues within 4Å: Chain A: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190, E.193 Chain G: V.45, S.46, L.49, F.50, A.53, H.83 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain G Hydrophobic interactions: A:L.24, A:I.29, A:Y.61, A:Y.63, A:I.93, G:V.45, G:L.49, G:L.49, G:A.53 Water bridges: A:D.27, A:D.27, A:Y.61 Halogen bonds: A:R.23 Z53.3: 17 residues within 4Å: Chain A: V.45, S.46, L.49, F.50, Q.52, A.53, H.83 Chain B: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 15 PLIP interactions: 5 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:V.45, A:L.49, A:L.49, A:A.53, B:L.24, B:I.29, B:Y.61, B:Y.63, B:I.91, B:I.91, B:I.93 Water bridges: A:Q.52, B:D.27, B:D.27 Halogen bonds: B:R.23 Z53.4: 17 residues within 4Å: Chain B: V.45, S.46, L.49, F.50, Q.52, A.53, H.83 Chain C: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 14 PLIP interactions: 4 interactions with chain B, 10 interactions with chain C Hydrophobic interactions: B:V.45, B:L.49, B:L.49, B:A.53, C:L.24, C:D.27, C:I.29, C:Y.61, C:Y.63, C:I.91, C:I.91, C:I.93 Water bridges: C:D.27, C:D.27 Z53.6: 15 residues within 4Å: Chain C: V.45, S.46, L.49, F.50, A.53, H.83 Chain D: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93 14 PLIP interactions: 9 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:L.24, D:I.29, D:Y.61, D:Y.63, D:I.91, D:I.91, D:I.93, C:V.45, C:L.49, C:L.49, C:A.53 Water bridges: D:D.27, D:D.27, C:Q.52 Z53.8: 16 residues within 4Å: Chain D: V.45, S.46, L.49, F.50, A.53, H.83 Chain E: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 16 PLIP interactions: 5 interactions with chain D, 11 interactions with chain E Hydrophobic interactions: D:V.45, D:L.49, D:L.49, D:A.53, E:L.24, E:I.29, E:Y.61, E:Y.63, E:I.91, E:I.91, E:I.93 Water bridges: D:Q.52, E:D.27, E:D.27, E:Y.61 Halogen bonds: E:R.23 Z53.10: 16 residues within 4Å: Chain E: V.45, S.46, L.49, F.50, A.53, H.83 Chain F: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 15 PLIP interactions: 5 interactions with chain E, 10 interactions with chain F Hydrophobic interactions: E:V.45, E:L.49, E:L.49, E:A.53, F:L.24, F:I.29, F:Y.61, F:Y.63, F:I.91, F:I.91, F:I.93 Water bridges: E:Q.52, F:D.27, F:D.27, F:Y.61 Z53.12: 16 residues within 4Å: Chain F: V.45, S.46, L.49, F.50, A.53, H.83 Chain G: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 16 PLIP interactions: 11 interactions with chain G, 5 interactions with chain F Hydrophobic interactions: G:L.24, G:I.29, G:Y.61, G:Y.63, G:I.91, G:I.91, G:I.93, F:V.45, F:L.49, F:L.49, F:A.53 Water bridges: G:D.27, G:D.27, G:Y.61, F:Q.52 Halogen bonds: G:R.23 Z53.14: 16 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, S.46, L.49, F.50, A.53, H.83 11 PLIP interactions: 4 interactions with chain N, 7 interactions with chain H Hydrophobic interactions: N:V.45, N:L.49, N:A.53, H:L.24, H:Y.61, H:Y.63, H:I.91, H:I.91, H:I.93 Water bridges: N:Q.52 Halogen bonds: H:R.23 Z53.16: 16 residues within 4Å: Chain H: V.45, S.46, L.49, F.50, A.53, H.83 Chain I: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 15 PLIP interactions: 10 interactions with chain I, 5 interactions with chain H Hydrophobic interactions: I:L.24, I:I.29, I:Y.61, I:Y.63, I:I.91, I:I.91, I:I.93, H:V.45, H:L.49, H:L.49, H:A.53 Water bridges: I:D.27, I:D.27, H:Q.52 Halogen bonds: I:R.23 Z53.18: 16 residues within 4Å: Chain I: V.45, S.46, L.49, F.50, A.53, H.83 Chain J: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 13 PLIP interactions: 8 interactions with chain J, 5 interactions with chain I Hydrophobic interactions: J:L.24, J:I.29, J:Y.61, J:Y.63, J:I.91, J:I.91, J:I.93, I:V.45, I:L.49, I:L.49, I:A.53 Halogen bonds: J:R.23 Water bridges: I:Q.52 Z53.20: 16 residues within 4Å: Chain J: V.45, S.46, L.49, F.50, A.53, H.83 Chain K: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 14 PLIP interactions: 10 interactions with chain K, 4 interactions with chain J Hydrophobic interactions: K:L.24, K:I.29, K:Y.61, K:Y.63, K:I.91, K:I.91, K:I.93, J:V.45, J:L.49, J:L.49, J:A.53 Water bridges: K:D.27, K:D.27, K:Q.89 Z53.22: 17 residues within 4Å: Chain K: V.45, S.46, L.49, F.50, A.53, H.83 Chain L: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190, E.193 12 PLIP interactions: 8 interactions with chain L, 4 interactions with chain K Hydrophobic interactions: L:L.24, L:I.29, L:Y.61, L:Y.63, L:I.93, K:V.45, K:L.49, K:L.49, K:A.53 Water bridges: L:D.27, L:D.27 Halogen bonds: L:R.23 Z53.24: 16 residues within 4Å: Chain L: V.45, S.46, L.49, F.50, A.53, H.83 Chain M: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 14 PLIP interactions: 9 interactions with chain M, 5 interactions with chain L Hydrophobic interactions: M:L.24, M:I.29, M:Y.61, M:Y.63, M:I.91, M:I.91, M:I.93, L:V.45, L:L.49, L:L.49, L:A.53 Hydrogen bonds: M:D.27 Water bridges: M:Y.61, L:Q.52 Z53.26: 17 residues within 4Å: Chain M: V.45, S.46, L.49, F.50, Q.52, A.53, H.83 Chain N: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 12 PLIP interactions: 3 interactions with chain M, 9 interactions with chain N Hydrophobic interactions: M:V.45, M:L.49, M:A.53, N:L.24, N:I.29, N:Y.61, N:Y.63, N:I.91, N:I.91, N:I.93 Water bridges: N:Y.61 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 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.81, A:P.86, H2O.5 MG.5: 4 residues within 4Å: Chain C: I.81, I.84, P.86, V.88 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:I.81, C:P.86, H2O.15 MG.7: 3 residues within 4Å: Chain D: I.81, I.84, P.86 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:I.81, D:P.86, H2O.19, H2O.20 MG.9: 3 residues within 4Å: Chain E: I.81, I.84, P.86 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:I.81, E:P.86, H2O.25, H2O.26 MG.11: 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.32, H2O.32 MG.13: 4 residues within 4Å: Chain A: K.195 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.4, H2O.39 MG.15: 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.42, H2O.43 MG.17: 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.49, H2O.49 MG.19: 3 residues within 4Å: Chain J: I.81, I.84, P.86 5 PLIP interactions: 2 interactions with chain J, 3 Ligand-Water interactions Metal complexes: J:I.81, J:P.86, H2O.51, H2O.55, H2O.55 MG.21: 3 residues within 4Å: Chain K: I.81, I.84, P.86 4 PLIP interactions: 2 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:I.81, K:P.86, H2O.61, H2O.65 MG.23: 4 residues within 4Å: Chain L: I.81, I.84, P.86, V.88 4 PLIP interactions: 2 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:I.81, L:P.86, H2O.64, H2O.67 MG.25: 3 residues within 4Å: Chain M: I.81, I.84, P.86 4 PLIP interactions: 2 interactions with chain M, 2 Ligand-Water interactions Metal complexes: M:I.81, M:P.86, H2O.71, H2O.71

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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