SMTL ID : 8e71.1

Staphylococcus aureus ClpP in complex with compound 3471

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-14-mer

Ligands

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

MPD.1: 10 residues within 4Å: Chain A: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154, T.169 Ligand excluded by PLIP MPD.3: 8 residues within 4Å: Chain B: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 Ligand excluded by PLIP MPD.5: 8 residues within 4Å: Chain C: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 Ligand excluded by PLIP MPD.7: 8 residues within 4Å: Chain D: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 Ligand excluded by PLIP MPD.9: 8 residues within 4Å: Chain E: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 Ligand excluded by PLIP MPD.11: 8 residues within 4Å: Chain F: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 Ligand excluded by PLIP MPD.13: 4 residues within 4Å: Chain A: F.50, A.53, Q.54 Chain G: R.23 Ligand excluded by PLIP MPD.14: 8 residues within 4Å: Chain G: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 Ligand excluded by PLIP MPD.16: 8 residues within 4Å: Chain H: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 Ligand excluded by PLIP MPD.18: 8 residues within 4Å: Chain I: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 Ligand excluded by PLIP MPD.20: 9 residues within 4Å: Chain J: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 Ligand excluded by PLIP MPD.22: 8 residues within 4Å: Chain K: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 Ligand excluded by PLIP MPD.24: 8 residues within 4Å: Chain L: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 Ligand excluded by PLIP MPD.26: 8 residues within 4Å: Chain M: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 Ligand excluded by PLIP MPD.27: 5 residues within 4Å: Chain M: R.23 Chain N: F.50, A.53, Q.54 Ligands: USU.28 Ligand excluded by PLIP MPD.29: 9 residues within 4Å: Chain N: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 Ligand excluded by PLIP

14 x USU: (5S,6S,9aS)-N-[(4-fluorophenyl)methyl]-6-methyl-8-[(naphthalen-1-yl)methyl]-4,7-dioxohexahydro-2H-pyrazino[1,2-a]pyrimidine-1(6H)-carboxamide(Non-covalent)

USU.2: 15 residues within 4Å: Chain A: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Chain B: V.45, L.49, F.50, A.53, T.80, H.83 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.24, A:D.27, A:I.29, A:I.29, A:Y.61, A:Y.63, A:I.91, A:I.91, A:I.93, B:V.45, B:L.49, B:A.53 Water bridges: A:D.27, A:D.27, B:Q.52 USU.4: 14 residues within 4Å: Chain B: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Chain C: V.45, L.49, F.50, A.53, H.83 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:L.24, B:D.27, B:I.29, B:I.29, B:Y.61, B:Y.63, B:I.91, B:I.91, B:I.93, C:V.45, C:L.49, C:A.53 Water bridges: B:D.27, B:D.27 USU.6: 14 residues within 4Å: Chain C: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Chain D: V.45, L.49, F.50, A.53, H.83 15 PLIP interactions: 4 interactions with chain D, 11 interactions with chain C Hydrophobic interactions: D:V.45, D:L.49, D:L.49, D:A.53, C:L.24, C:D.27, C:I.29, 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 USU.8: 14 residues within 4Å: Chain D: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Chain E: V.45, L.49, F.50, A.53, H.83 15 PLIP interactions: 4 interactions with chain E, 11 interactions with chain D Hydrophobic interactions: E:V.45, E:L.49, E:A.53, D:L.24, D:D.27, D:I.29, D:I.29, D:Y.61, D:Y.63, D:I.91, D:I.91, D:I.93 Water bridges: E:Q.52, D:D.27, D:D.27 USU.10: 14 residues within 4Å: Chain E: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Chain F: V.45, L.49, F.50, A.53, H.83 16 PLIP interactions: 12 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: E:L.24, E:D.27, E:I.29, E:I.29, E:Y.61, E:Y.63, E:I.91, E:I.91, E:I.93, F:V.45, F:L.49, F:L.49, F:A.53 Water bridges: E:D.27, E:D.27, E:Y.61 USU.12: 14 residues within 4Å: Chain F: 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, A.53, H.83 16 PLIP interactions: 11 interactions with chain F, 5 interactions with chain G Hydrophobic interactions: F:L.24, F:D.27, F:I.29, F:I.29, F:Y.61, F:Y.63, F:I.91, F:I.91, F:I.93, G:V.45, G:L.49, G:L.49, G:A.53 Water bridges: F:D.27, F:D.27, G:Q.52 USU.15: 15 residues within 4Å: Chain A: V.45, 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 16 PLIP interactions: 5 interactions with chain A, 11 interactions with chain G Hydrophobic interactions: A:V.45, A:L.49, A:L.49, A:A.53, G:L.24, G:D.27, G:I.29, G:I.29, G:Y.61, G:Y.63, G:I.91, G:I.91, G:I.93 Water bridges: A:Q.52, G:D.27, G:D.27 USU.17: 14 residues within 4Å: Chain H: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Chain I: V.45, L.49, F.50, A.53, H.83 16 PLIP interactions: 12 interactions with chain H, 4 interactions with chain I Hydrophobic interactions: H:L.24, H:D.27, H:I.29, H:I.29, H:Y.61, H:Y.63, H:I.91, H:I.91, H:I.93, I:V.45, I:L.49, I:A.53 Water bridges: H:D.27, H:D.27, H:Y.61, I:Q.52 USU.19: 15 residues within 4Å: Chain I: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Chain J: V.45, L.49, F.50, A.53, T.80, H.83 15 PLIP interactions: 12 interactions with chain I, 3 interactions with chain J Hydrophobic interactions: I:L.24, I:D.27, I:I.29, I:I.29, I:Y.61, I:Y.63, I:I.91, I:I.91, I:I.93, J:V.45, J:L.49, J:A.53 Water bridges: I:D.27, I:D.27, I:Y.61 USU.21: 14 residues within 4Å: Chain J: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Chain K: V.45, L.49, F.50, A.53, H.83 14 PLIP interactions: 9 interactions with chain J, 5 interactions with chain K Hydrophobic interactions: J:L.24, J:I.29, J:I.29, J:Y.61, J:Y.63, J:I.91, J:I.91, J:I.93, K:V.45, K:L.49, K:L.49, K:A.53 Water bridges: J:D.27, K:Q.52 USU.23: 14 residues within 4Å: Chain K: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Chain L: V.45, L.49, F.50, A.53, H.83 15 PLIP interactions: 11 interactions with chain K, 4 interactions with chain L Hydrophobic interactions: K:L.24, K:D.27, K:I.29, K:I.29, K:Y.61, K:Y.63, K:I.91, K:I.91, K:I.93, L:V.45, L:L.49, L:L.49, L:A.53 Water bridges: K:D.27, K:D.27 USU.25: 14 residues within 4Å: Chain L: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Chain M: V.45, L.49, F.50, A.53, H.83 18 PLIP interactions: 6 interactions with chain M, 12 interactions with chain L Hydrophobic interactions: M:V.45, M:L.49, M:L.49, M:L.49, M:A.53, L:L.24, L:D.27, L:I.29, L:I.29, L:Y.61, L:Y.63, L:I.91, L:I.91, L:I.93 Water bridges: M:Q.52, L:D.27, L:D.27, L:Y.61 USU.28: 15 residues within 4Å: Chain M: 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, A.53, H.83 Ligands: MPD.27 15 PLIP interactions: 3 interactions with chain N, 12 interactions with chain M Hydrophobic interactions: N:V.45, N:L.49, N:A.53, M:L.24, M:D.27, M:I.29, M:I.29, M:Y.61, M:Y.63, M:I.91, M:I.91, M:I.93 Water bridges: M:D.27, M:D.27, M:Y.61 USU.30: 14 residues within 4Å: Chain H: V.45, L.49, F.50, A.53, H.83 Chain N: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 16 PLIP interactions: 12 interactions with chain N, 4 interactions with chain H Hydrophobic interactions: N:L.24, N:D.27, N:I.29, N:I.29, N:Y.61, N:Y.63, N:I.91, N:I.91, N:I.93, H:V.45, H:L.49, H:A.53 Water bridges: N:D.27, N:D.27, N:Y.61, H:Q.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, A.C. et al., Development of a high throughput and site specific, fluorescent polarization assay to screen for activators of Caseinolytic Protease P leads to the discovery of synthetically tractable new activator class. To Be Published

Release Date

2023-07-05

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
I

I
K

J
L

K
M

L
N

M
S

N
T

ATP-dependent Clp protease proteolytic subunit

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