SMTL ID : 7vp9.1

Crystal structure of human ClpP in complex with ZG111

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-14-mer

Ligands

14 x 7SR: (6S,9aS)-N-[(4-bromophenyl)methyl]-6-[(2S)-butan-2-yl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide(Non-covalent)

7SR.1: 15 residues within 4Å: Chain A: I.19, R.22, L.23, E.26, I.28, Y.62, W.90, L.114 Chain G: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 17 PLIP interactions: 9 interactions with chain A, 8 interactions with chain G Hydrophobic interactions: A:R.22, A:L.23, A:E.26, A:I.28, A:Y.62, A:L.114, G:I.44, G:L.48, G:L.48, G:L.48, G:F.49, G:Y.82, G:Y.82 Hydrogen bonds: A:E.26, G:Q.51 pi-Stacking: A:W.90 Halogen bonds: A:I.19 7SR.2: 14 residues within 4Å: Chain A: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain B: I.19, R.22, L.23, E.26, I.28, Y.62, W.90 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.23, B:E.26, B:I.28, B:I.28, B:Y.62, A:I.44, A:L.48, A:L.48, A:F.49, A:Y.82 Hydrogen bonds: B:E.26 pi-Stacking: B:W.90 Halogen bonds: B:I.19 7SR.4: 11 residues within 4Å: Chain B: L.48, F.49, Q.51, S.52, Y.82 Chain C: I.19, E.26, I.28, W.90, L.114, P.192 15 PLIP interactions: 5 interactions with chain B, 10 interactions with chain C Hydrophobic interactions: B:L.48, B:L.48, B:L.48, B:F.49, B:Y.82, C:E.26, C:I.28, C:I.28, C:W.90, C:L.114, C:P.192, C:P.192 Hydrogen bonds: C:E.26 pi-Stacking: C:W.90 Halogen bonds: C:I.19 7SR.7: 13 residues within 4Å: Chain D: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain E: I.19, R.22, L.23, E.26, I.28, W.90 11 PLIP interactions: 4 interactions with chain E, 7 interactions with chain D Hydrophobic interactions: E:R.22, E:I.28, D:I.44, D:L.48, D:L.48, D:L.48, D:F.49, D:Y.82, D:Y.82 pi-Stacking: E:W.90 Halogen bonds: E:I.19 7SR.8: 10 residues within 4Å: Chain C: L.48, F.49, Q.51, S.52, Y.82 Chain D: I.19, R.22, I.28, W.90, L.114 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:L.48, C:L.48, C:F.49, C:Y.82, D:I.28, D:I.28, D:W.90, D:L.114 pi-Stacking: D:W.90 Halogen bonds: D:I.19 7SR.10: 14 residues within 4Å: Chain E: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain F: I.19, R.22, L.23, I.28, Y.62, W.90, P.192 13 PLIP interactions: 7 interactions with chain F, 6 interactions with chain E Hydrophobic interactions: F:L.23, F:I.28, F:Y.62, F:P.192, F:P.192, E:I.44, E:L.48, E:L.48, E:L.48, E:F.49, E:Y.82 pi-Stacking: F:W.90 Halogen bonds: F:I.19 7SR.13: 15 residues within 4Å: Chain F: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain G: I.19, R.22, L.23, E.26, I.28, Y.62, W.90, P.192 14 PLIP interactions: 6 interactions with chain F, 8 interactions with chain G Hydrophobic interactions: F:I.44, F:L.48, F:L.48, F:L.48, F:F.49, F:Y.82, G:L.23, G:E.26, G:I.28, G:Y.62, G:P.192 Hydrogen bonds: G:E.26 pi-Stacking: G:W.90 Halogen bonds: G:I.19 7SR.15: 14 residues within 4Å: Chain H: I.19, 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 18 PLIP interactions: 9 interactions with chain H, 9 interactions with chain N Hydrophobic interactions: H:R.22, H:L.23, H:E.26, H:I.28, H:Y.62, N:I.44, N:L.48, N:L.48, N:L.48, N:F.49, N:Y.82, N:Y.82 Hydrogen bonds: H:E.26, H:E.26, N:Q.51, N:Y.82 pi-Stacking: H:W.90 Halogen bonds: H:I.19 7SR.17: 16 residues within 4Å: Chain I: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain J: I.19, R.22, L.23, E.26, I.28, Y.62, W.90, V.92, L.114 20 PLIP interactions: 12 interactions with chain J, 8 interactions with chain I Hydrophobic interactions: J:R.22, J:L.23, J:E.26, J:I.28, J:Y.62, J:Y.62, J:W.90, J:V.92, J:L.114, I:I.44, I:L.48, I:L.48, I:L.48, I:F.49, I:Y.82, I:Y.82 Hydrogen bonds: J:E.26, I:Y.82 pi-Stacking: J:W.90 Halogen bonds: J:I.19 7SR.18: 12 residues within 4Å: Chain H: L.48, F.49, Q.51, S.52, Y.82 Chain I: I.19, R.22, L.23, E.26, I.28, Y.62, W.90 18 PLIP interactions: 11 interactions with chain I, 7 interactions with chain H Hydrophobic interactions: I:R.22, I:L.23, I:E.26, I:I.28, I:Y.62, I:Y.62, I:W.90, H:L.48, H:L.48, H:L.48, H:F.49, H:Y.82, H:Y.82 Hydrogen bonds: I:E.26, I:E.26, H:Y.82 pi-Stacking: I:W.90 Halogen bonds: I:I.19 7SR.21: 13 residues within 4Å: Chain K: L.48, F.49, Q.51, S.52, Y.82 Chain L: I.19, R.22, L.23, E.26, I.28, Y.62, W.90, L.114 18 PLIP interactions: 9 interactions with chain K, 9 interactions with chain L Hydrophobic interactions: K:L.48, K:L.48, K:L.48, K:F.49, K:F.49, K:Y.82, K:Y.82, L:R.22, L:L.23, L:E.26, L:I.28, L:Y.62, L:L.114 Hydrogen bonds: K:Q.51, K:Y.82, L:E.26 pi-Stacking: L:W.90 Halogen bonds: L:I.19 7SR.22: 15 residues within 4Å: Chain J: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain K: I.19, R.22, L.23, E.26, I.28, Y.62, W.90, L.114 20 PLIP interactions: 12 interactions with chain K, 8 interactions with chain J Hydrophobic interactions: K:R.22, K:L.23, K:E.26, K:I.28, K:Y.62, K:Y.62, K:W.90, K:L.114, J:I.44, J:L.48, J:L.48, J:L.48, J:F.49, J:Y.82, J:Y.82 Hydrogen bonds: K:E.26, K:E.26, J:Y.82 pi-Stacking: K:W.90 Halogen bonds: K:I.19 7SR.24: 15 residues within 4Å: Chain L: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain M: I.19, R.22, L.23, E.26, I.28, Y.62, W.90, L.114 17 PLIP interactions: 8 interactions with chain M, 9 interactions with chain L Hydrophobic interactions: M:R.22, M:L.23, M:I.28, M:Y.62, M:Y.62, M:L.114, L:I.44, L:L.48, L:L.48, L:L.48, L:F.49, L:Y.82, L:Y.82 pi-Stacking: M:W.90 Halogen bonds: M:I.19 Hydrogen bonds: L:Q.51, L:Y.82 7SR.27: 13 residues within 4Å: Chain M: L.48, F.49, Q.51, S.52, Y.82 Chain N: I.19, R.22, L.23, E.26, I.28, Y.62, W.90, L.114 18 PLIP interactions: 12 interactions with chain N, 6 interactions with chain M Hydrophobic interactions: N:R.22, N:L.23, N:E.26, N:I.28, N:Y.62, N:Y.62, N:W.90, N:L.114, M:L.48, M:L.48, M:L.48, M:Y.82, M:Y.82 Hydrogen bonds: N:E.26, N:E.26, M:Y.82 pi-Stacking: N:W.90 Halogen bonds: N:I.19

14 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: M.80, N.85, T.107 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain B: M.80, Q.81, I.83, N.85 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:I.83 MG.6: 4 residues within 4Å: Chain C: M.80, Q.81, I.83 Chain D: H.191 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:Q.81, C:I.83 MG.9: 4 residues within 4Å: Chain D: M.80, I.83, N.85, T.107 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain E: M.80, Q.81, I.83, N.85 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain F: M.80, Q.81, I.83, N.85 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:M.80 MG.14: 4 residues within 4Å: Chain G: M.80, Q.81, I.83, N.85 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:I.83, H2O.1 MG.16: 4 residues within 4Å: Chain H: M.80, Q.81, I.83, N.85 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:M.80, H:I.83, H2O.1 MG.19: 3 residues within 4Å: Chain I: M.80, I.83, N.85 3 PLIP interactions: 2 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:M.80, I:I.83, H2O.2 MG.20: 4 residues within 4Å: Chain J: M.80, Q.81, I.83, N.85 3 PLIP interactions: 2 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:M.80, J:I.83, H2O.2 MG.23: 1 residues within 4Å: Chain K: T.107 2 PLIP interactions: 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:T.107, H2O.2 MG.25: 4 residues within 4Å: Chain L: M.80, Q.81, I.83, N.85 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:M.80, L:I.83 MG.26: 3 residues within 4Å: Chain M: M.80, I.83, N.85 2 PLIP interactions: 1 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:N.85, H2O.2 MG.28: 3 residues within 4Å: Chain N: M.80, Q.81, T.107 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, P. et al., Aberrant human ClpP activation disturbs mitochondrial proteome homeostasis to suppress pancreatic ductal adenocarcinoma. Cell Chem Biol (2022)

Release Date

2022-06-08

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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