SMTL ID : 7uvm.1

Crystal structure of human ClpP protease in complex with TR-27

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-14-mer

Ligands

14 x OX0: (10R)-4-[(4-chlorophenyl)methyl]-7-[(3-ethynylphenyl)methyl]-2,4,6,7,8,9-hexahydroimidazo[1,2-a]pyrido[3,4-e]pyrimidin-5(1H)-one(Non-covalent)

OX0.1: 16 residues within 4Å: Chain A: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 Chain G: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain G Hydrophobic interactions: A:L.23, A:E.26, A:I.28, A:Y.62, A:Y.62, A:V.92, A:V.92, G:I.44, G:L.48 Hydrogen bonds: A:E.26 pi-Stacking: A:H.60, G:Y.82 Water bridges: G:Q.51, G:Y.82 OX0.2: 16 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, V.92, L.114 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.23, B:E.26, B:Y.62, B:Y.62, B:V.92, B:L.114, A:I.44, A:L.48 Hydrogen bonds: B:E.26, A:Q.51 pi-Stacking: A:Y.82 OX0.3: 16 residues within 4Å: Chain B: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain C: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:L.23, C:E.26, C:I.28, C:Y.62, C:Y.62, C:W.90, C:V.92, C:V.92, B:L.48, B:L.48 pi-Stacking: C:H.60, B:Y.82 Hydrogen bonds: B:Q.51 OX0.4: 19 residues within 4Å: Chain C: I.44, A.45, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain D: I.19, R.22, L.23, E.26, I.28, M.32, H.60, Y.62, W.90, V.92, L.114 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.23, D:E.26, D:I.28, D:Y.62, D:Y.62, D:V.92, D:V.92, D:L.114, C:L.48, C:L.48 pi-Stacking: D:H.60, C:Y.82 OX0.5: 17 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, R.27, I.28, H.60, Y.62, W.90, V.92, L.114 13 PLIP interactions: 9 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:L.23, E:E.26, E:I.28, E:Y.62, E:Y.62, E:W.90, E:V.92, E:L.114, D:I.44, D:L.48 pi-Stacking: E:H.60, D:Y.82 Hydrogen bonds: D:Q.51 OX0.6: 18 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, E.26, I.28, M.32, H.60, Y.62, W.90, V.92, L.114 12 PLIP interactions: 4 interactions with chain E, 8 interactions with chain F Hydrophobic interactions: E:I.44, E:L.48, E:L.48, F:L.23, F:E.26, F:I.28, F:Y.62, F:Y.62, F:V.92, F:V.92, F:L.114 pi-Stacking: E:Y.82 OX0.7: 18 residues within 4Å: Chain F: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain G: R.22, L.23, E.26, I.28, M.32, H.60, Y.62, W.90, V.92, L.114, L.189 15 PLIP interactions: 10 interactions with chain G, 5 interactions with chain F Hydrophobic interactions: G:L.23, G:E.26, G:I.28, G:Y.62, G:Y.62, G:W.90, G:V.92, G:V.92, F:I.44, F:L.48 Hydrogen bonds: G:E.26 pi-Stacking: G:H.60, F:Y.82 Water bridges: F:Q.51, F:Q.51 OX0.8: 16 residues within 4Å: Chain H: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 Chain N: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 13 PLIP interactions: 8 interactions with chain H, 5 interactions with chain N Hydrophobic interactions: H:L.23, H:E.26, H:I.28, H:Y.62, H:Y.62, H:V.92, H:V.92, N:I.44, N:L.48 pi-Stacking: H:H.60, N:Y.82 Water bridges: N:Q.51, N:Y.82 OX0.9: 16 residues within 4Å: Chain H: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain I: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 10 PLIP interactions: 6 interactions with chain I, 4 interactions with chain H Hydrophobic interactions: I:L.23, I:E.26, I:Y.62, I:Y.62, I:V.92, I:L.114, H:I.44, H:L.48 Hydrogen bonds: H:Q.51 pi-Stacking: H:Y.82 OX0.10: 16 residues within 4Å: Chain I: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain J: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 14 PLIP interactions: 4 interactions with chain I, 10 interactions with chain J Hydrophobic interactions: I:L.48, I:L.48, J:L.23, J:E.26, J:I.28, J:Y.62, J:Y.62, J:W.90, J:V.92, J:V.92 Hydrogen bonds: I:Q.51, J:E.26 pi-Stacking: I:Y.82, J:H.60 OX0.11: 19 residues within 4Å: Chain J: I.44, A.45, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain K: I.19, R.22, L.23, E.26, I.28, M.32, H.60, Y.62, W.90, V.92, L.114 13 PLIP interactions: 10 interactions with chain K, 3 interactions with chain J Hydrophobic interactions: K:L.23, K:E.26, K:I.28, K:Y.62, K:Y.62, K:V.92, K:V.92, K:L.114, J:L.48, J:L.48 Hydrogen bonds: K:E.26 pi-Stacking: K:H.60, J:Y.82 OX0.12: 17 residues within 4Å: Chain K: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain L: R.22, L.23, E.26, R.27, I.28, H.60, Y.62, W.90, V.92, L.114 14 PLIP interactions: 4 interactions with chain K, 10 interactions with chain L Hydrophobic interactions: K:I.44, K:L.48, L:L.23, L:E.26, L:I.28, L:Y.62, L:Y.62, L:W.90, L:V.92, L:L.114 Hydrogen bonds: K:Q.51, L:E.26 pi-Stacking: K:Y.82, L:H.60 OX0.13: 18 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, M.32, H.60, Y.62, W.90, V.92, L.114 13 PLIP interactions: 9 interactions with chain M, 4 interactions with chain L Hydrophobic interactions: M:L.23, M:E.26, M:I.28, M:Y.62, M:Y.62, M:V.92, M:V.92, M:L.114, L:I.44, L:L.48, L:L.48 Hydrogen bonds: M:E.26 pi-Stacking: L:Y.82 OX0.14: 18 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, M.32, H.60, Y.62, W.90, V.92, L.114, L.189 14 PLIP interactions: 5 interactions with chain M, 9 interactions with chain N Hydrophobic interactions: M:I.44, M:L.48, N:L.23, N:E.26, N:I.28, N:Y.62, N:Y.62, N:W.90, N:V.92, N:V.92 Water bridges: M:Q.51, M:Q.51 pi-Stacking: M:Y.82, N:H.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mabanglo, M.F. et al., Potent ClpP agonists with anticancer properties bind with improved structural complementarity and alter the mitochondrial N-terminome. Structure (2023)

Release Date

2023-01-11

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
A

I
B

J
C

K
D

L
E

M
F

N
G

ATP-dependent Clp protease proteolytic subunit, mitochondrial

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