SMTL ID : 7wh5.1

Crystal structure of human ClpP in complex with ZG180

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-14-mer

Ligands

14 x 9DF: (6S,9aS)-6-[(2S)-butan-2-yl]-8-(naphthalen-1-ylmethyl)-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)

9DF.1: 13 residues within 4Å: Chain A: R.22, L.23, E.26, I.28, Y.62, W.90 Chain G: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain G Hydrophobic interactions: A:E.26, A:I.28, A:Y.62, A:Y.62, G:I.44, G:L.48, G:L.48, G:Y.82 pi-Stacking: A:W.90 Halogen bonds: A:R.22 9DF.2: 14 residues within 4Å: Chain A: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain B: R.22, L.23, E.26, I.28, H.60, Y.62, W.90 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:E.26, B:I.28, B:Y.62, B:Y.62, A:I.44, A:L.48, A:L.48, A:T.79, A:Y.82, A:Y.82 pi-Stacking: B:W.90 Halogen bonds: B:R.22 9DF.3: 14 residues within 4Å: Chain C: L.48, F.49, Q.51, S.52, T.79, Y.82 Chain D: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, L.114 12 PLIP interactions: 7 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:E.26, D:I.28, D:Y.62, D:Y.62, D:L.114, C:L.48, C:L.48, C:Y.82, C:Y.82 pi-Stacking: D:W.90 Halogen bonds: D:R.22 Hydrogen bonds: C:Y.82 9DF.4: 14 residues within 4Å: Chain B: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82, I.83 Chain C: R.22, L.23, E.26, I.28, Y.62, W.90 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:L.23, C:E.26, C:I.28, C:I.28, C:Y.62, B:I.44, B:L.48, B:L.48, B:Y.82, B:I.83 pi-Stacking: C:W.90 Halogen bonds: C:R.22 Hydrogen bonds: B:Y.82 9DF.5: 14 residues within 4Å: Chain D: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain E: R.22, L.23, E.26, I.28, H.60, Y.62, W.90 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain E Hydrophobic interactions: D:I.44, D:L.48, D:Y.82, E:E.26, E:I.28, E:Y.62, E:Y.62 pi-Stacking: E:W.90 9DF.6: 13 residues within 4Å: Chain E: I.44, L.48, F.49, Q.51, S.52, Y.82 Chain F: R.22, L.23, E.26, I.28, H.60, Y.62, W.90 10 PLIP interactions: 6 interactions with chain F, 4 interactions with chain E Hydrophobic interactions: F:E.26, F:I.28, F:I.28, F:H.60, F:Y.62, E:I.44, E:L.48, E:L.48, E:Y.82 pi-Stacking: F:W.90 9DF.7: 12 residues within 4Å: Chain F: I.44, L.48, F.49, Q.51, S.52, Y.82 Chain G: R.22, L.23, E.26, I.28, Y.62, W.90 10 PLIP interactions: 7 interactions with chain G, 3 interactions with chain F Hydrophobic interactions: G:L.23, G:E.26, G:I.28, G:Y.62, G:Y.62, F:I.44, F:L.48, F:Y.82 pi-Stacking: G:W.90 Halogen bonds: G:R.22 9DF.8: 13 residues within 4Å: Chain H: R.22, L.23, E.26, I.28, Y.62, W.90 Chain N: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 12 PLIP interactions: 6 interactions with chain H, 6 interactions with chain N Hydrophobic interactions: H:E.26, H:I.28, H:Y.62, H:Y.62, N:I.44, N:L.48, N:L.48, N:Y.82, N:Y.82 pi-Stacking: H:W.90 Halogen bonds: H:R.22 Hydrogen bonds: N:Y.82 9DF.9: 14 residues within 4Å: Chain H: I.44, A.45, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain I: R.22, L.23, E.26, I.28, Y.62, W.90 11 PLIP interactions: 5 interactions with chain I, 6 interactions with chain H Hydrophobic interactions: I:E.26, I:Y.62, I:Y.62, H:I.44, H:L.48, H:L.48, H:Y.82, H:Y.82 Hydrogen bonds: I:E.26, H:Y.82 pi-Stacking: I:W.90 9DF.10: 12 residues within 4Å: Chain I: L.48, F.49, Q.51, S.52, Y.82 Chain J: R.22, L.23, E.26, I.28, H.60, Y.62, W.90 8 PLIP interactions: 6 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: J:E.26, J:I.28, J:H.60, J:Y.62, I:L.48, I:Y.82 pi-Stacking: J:W.90 Halogen bonds: J:R.22 9DF.11: 14 residues within 4Å: Chain J: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain K: R.22, L.23, E.26, I.28, H.60, Y.62, W.90 11 PLIP interactions: 6 interactions with chain K, 5 interactions with chain J Hydrophobic interactions: K:E.26, K:I.28, K:Y.62, K:Y.62, J:I.44, J:L.48, J:L.48, J:Y.82, J:Y.82 pi-Stacking: K:W.90 Halogen bonds: K:R.22 9DF.12: 13 residues within 4Å: Chain K: L.48, F.49, Q.51, S.52, T.79, Y.82 Chain L: R.22, L.23, E.26, I.28, Y.62, W.90, V.92 12 PLIP interactions: 8 interactions with chain L, 4 interactions with chain K Hydrophobic interactions: L:L.23, L:E.26, L:I.28, L:Y.62, L:Y.62, L:V.92, K:L.48, K:Y.82, K:Y.82 pi-Stacking: L:W.90 Halogen bonds: L:R.22 Hydrogen bonds: K:Y.82 9DF.13: 14 residues within 4Å: Chain L: L.48, F.49, Q.51, S.52, T.79, Y.82, I.83 Chain M: R.22, L.23, E.26, I.28, H.60, Y.62, W.90 9 PLIP interactions: 5 interactions with chain M, 4 interactions with chain L Hydrophobic interactions: M:E.26, M:I.28, M:Y.62, L:L.48, L:L.48, L:I.83 pi-Stacking: M:W.90 Halogen bonds: M:R.22 Hydrogen bonds: L:Y.82 9DF.14: 13 residues within 4Å: Chain M: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain N: R.22, L.23, E.26, I.28, Y.62, W.90 11 PLIP interactions: 6 interactions with chain N, 5 interactions with chain M Hydrophobic interactions: N:E.26, N:I.28, N:Y.62, N:Y.62, M:I.44, M:L.48, M:L.48, M:Y.82 pi-Stacking: N:W.90 Halogen bonds: N:R.22 Hydrogen bonds: M:Y.82

1 x MG: MAGNESIUM ION(Non-covalent)

MG.15: 3 residues within 4Å: Chain N: M.80, Q.81, I.83 3 PLIP interactions: 2 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:Q.81, N:I.83, H2O.9

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, mitochondrial: 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, mitochondrial

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