SMTL ID : 8e7p.1

Staphylococcus aureus ClpP in complex with compound 3421

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-14-mer

Ligands

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

MPD.1: 8 residues within 4Å: Chain A: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.71, A:I.122, A:L.150 Hydrogen bonds: A:H.123 MPD.4: 8 residues within 4Å: Chain B: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.71, B:I.122, B:L.150 Hydrogen bonds: B:H.123 MPD.6: 8 residues within 4Å: Chain C: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.71, C:I.122, C:L.150 Hydrogen bonds: C:H.123 MPD.7: 8 residues within 4Å: Chain D: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.71, D:I.122, D:L.150 Hydrogen bonds: D:H.123 MPD.8: 5 residues within 4Å: Chain D: R.23 Chain E: F.50, A.53, Q.54 Ligands: UTC.9 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:F.50, E:A.53 Water bridges: E:Q.54 Hydrogen bonds: D:R.23 MPD.10: 9 residues within 4Å: Chain E: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:V.71, E:I.122, E:L.150, E:L.154 Hydrogen bonds: E:H.123 MPD.12: 10 residues within 4Å: Chain F: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154, T.169 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:V.71, F:I.122, F:L.150, F:T.169 Hydrogen bonds: F:H.123 MPD.14: 8 residues within 4Å: Chain G: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:V.71, G:I.122, G:L.150 Hydrogen bonds: G:H.123 MPD.15: 8 residues within 4Å: Chain H: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:V.71, H:I.122, H:L.150 Hydrogen bonds: H:H.123 MPD.18: 8 residues within 4Å: Chain I: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:V.71, I:I.122, I:L.150 Hydrogen bonds: I:H.123 MPD.20: 8 residues within 4Å: Chain J: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:V.71, J:I.122, J:L.150 Hydrogen bonds: J:H.123 MPD.22: 8 residues within 4Å: Chain K: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 5 PLIP interactions: 5 interactions with chain K Hydrophobic interactions: K:V.71, K:I.122, K:L.150 Hydrogen bonds: K:H.123 Water bridges: K:M.99 MPD.24: 9 residues within 4Å: Chain L: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, T.169 5 PLIP interactions: 5 interactions with chain L Hydrophobic interactions: L:V.71, L:I.122, L:L.150, L:T.169 Hydrogen bonds: L:H.123 MPD.26: 8 residues within 4Å: Chain M: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 4 PLIP interactions: 4 interactions with chain M Hydrophobic interactions: M:V.71, M:I.122, M:L.150 Hydrogen bonds: M:H.123 MPD.28: 8 residues within 4Å: Chain N: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 4 PLIP interactions: 4 interactions with chain N Hydrophobic interactions: N:V.71, N:I.122, N:L.150 Hydrogen bonds: N:H.123

13 x UTC: (5R,6S,9aS)-N-benzyl-6-[(4-hydroxyphenyl)methyl]-8-[(naphthalen-1-yl)methyl]-4,7-dioxohexahydro-2H-pyrazino[1,2-a]pyrimidine-1(6H)-carboxamide(Non-covalent)

UTC.2: 15 residues within 4Å: Chain A: V.45, 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: 10 interactions with chain G, 6 interactions with chain A Hydrophobic interactions: G:L.24, G:D.27, G:I.29, G:I.29, G:Y.61, G:Y.63, G:Y.63, G:I.93, A:V.45, A:L.49, A:L.49, A:F.50, A:A.53 Hydrogen bonds: G:D.27, G:D.27 Water bridges: A:Q.52 UTC.3: 13 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: L.49, F.50, A.53, H.83 12 PLIP interactions: 9 interactions with chain A, 3 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.93, B:L.49, B:L.49, B:A.53 Hydrogen bonds: A:D.27 Water bridges: A:Y.61 UTC.5: 15 residues within 4Å: Chain B: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 Chain C: V.45, L.49, F.50, A.53, H.83 15 PLIP interactions: 5 interactions with chain C, 10 interactions with chain B Hydrophobic interactions: C:V.45, C:L.49, C:L.49, C:F.50, C:A.53, B:L.24, B:D.27, B:I.29, B:I.29, B:Y.61, B:Y.63, B:Y.63, B:I.93 Hydrogen bonds: B:D.27 Water bridges: B:Y.61 UTC.9: 16 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, K.85 Ligands: MPD.8 14 PLIP interactions: 8 interactions with chain D, 6 interactions with chain E Hydrophobic interactions: D:L.24, D:D.27, D:I.29, D:I.29, D:Y.61, D:Y.63, D:I.93, E:V.45, E:L.49, E:L.49, E:A.53 Water bridges: D:D.27 Hydrogen bonds: E:K.85, E:K.85 UTC.11: 15 residues within 4Å: Chain E: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 Chain F: V.45, L.49, F.50, A.53, H.83 15 PLIP interactions: 10 interactions with chain E, 5 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:Y.63, E:I.93, F:V.45, F:L.49, F:F.50, F:A.53 Hydrogen bonds: E:D.27, E:D.27 Water bridges: F:Q.52 UTC.13: 16 residues within 4Å: Chain F: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 Chain G: V.45, L.49, F.50, A.53, T.80, H.83 13 PLIP interactions: 5 interactions with chain G, 8 interactions with chain F Hydrophobic interactions: G:V.45, G:L.49, G:L.49, G:A.53, F:L.24, F:D.27, F:I.29, F:I.29, F:Y.61, F:Y.63, F:Y.63, F:I.93 Water bridges: G:Q.52 UTC.16: 15 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, M.31, Y.61, Y.63, I.91, I.93, M.190 16 PLIP interactions: 6 interactions with chain H, 10 interactions with chain N Hydrophobic interactions: H:V.45, H:L.49, H:L.49, H:A.53, N:L.24, N:D.27, N:I.29, N:I.29, N:Y.61, N:Y.63, N:Y.63, N:I.93 Hydrogen bonds: H:K.85, H:K.85, N:D.27, N:D.27 UTC.17: 13 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: L.49, F.50, A.53, H.83 15 PLIP interactions: 5 interactions with chain I, 10 interactions with chain H Hydrophobic interactions: I:L.49, I:L.49, I:F.50, I:A.53, H:L.24, H:D.27, H:I.29, H:I.29, H:Y.61, H:Y.63, H:Y.63, H:I.93 Water bridges: I:Q.52 Hydrogen bonds: H:D.27, H:D.27 UTC.19: 14 residues within 4Å: Chain I: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 Chain J: L.49, F.50, A.53, H.83 16 PLIP interactions: 4 interactions with chain J, 12 interactions with chain I Hydrophobic interactions: J:L.49, J:L.49, J:F.50, J:A.53, I:L.24, I:D.27, I:I.29, I:I.29, I:Y.61, I:Y.63, I:Y.63, I:I.91, I:I.91, I:I.93 Hydrogen bonds: I:D.27, I:D.27 UTC.21: 14 residues within 4Å: Chain J: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 Chain K: L.49, F.50, A.53, H.83 13 PLIP interactions: 9 interactions with chain J, 4 interactions with chain K Hydrophobic interactions: J:L.24, J:D.27, J:I.29, J:I.29, J:Y.61, J:Y.63, J:Y.63, J:I.93, K:L.49, K:L.49, K:A.53 Water bridges: J:Y.61, K:Q.52 UTC.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: 7 interactions with chain L, 8 interactions with chain K Hydrophobic interactions: L:V.45, L:L.49, L:L.49, L:F.50, L:A.53, K:L.24, K:D.27, K:I.29, K:I.29, K:Y.61, K:Y.63, K:I.93 Water bridges: L:K.85, L:K.85, K:Y.61 UTC.25: 15 residues within 4Å: Chain L: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 Chain M: V.45, L.49, F.50, A.53, H.83 14 PLIP interactions: 5 interactions with chain M, 9 interactions with chain L Hydrophobic interactions: M:V.45, M:L.49, M:L.49, M:F.50, M:A.53, L:L.24, L:D.27, L:I.29, L:I.29, L:Y.61, L:Y.63, L:Y.63, L:I.93 Water bridges: L:Y.61 UTC.27: 14 residues within 4Å: Chain M: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 Chain N: L.49, F.50, A.53, H.83 14 PLIP interactions: 5 interactions with chain N, 9 interactions with chain M Hydrophobic interactions: N:L.49, N:L.49, N:F.50, N:A.53, M:L.24, M:D.27, M:I.29, M:I.29, M:Y.61, M:Y.63, M:Y.63, M:I.93 Water bridges: N:Q.52, M:D.27

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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