SMTL ID : 7uvu.1

Crystal structure of human ClpP protease in complex with TR-107

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.24 Å

Oligo State

homo-14-mer

Ligands

14 x OY9: 3-({3-[(4-chlorophenyl)methyl]-4-oxo-3,5,7,8-tetrahydropyrido[4,3-d]pyrimidin-6(4H)-yl}methyl)benzonitrile(Non-covalent)

OY9.1: 14 residues within 4Å: Chain A: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92 Chain G: I.44, L.48, F.49, S.52, T.79, Y.82 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain G Hydrophobic interactions: A:L.23, A:E.26, A:Y.62, A:Y.62, G:I.44, G:L.48, G:Y.82, G:Y.82 Hydrogen bonds: A:Y.62 pi-Stacking: A:H.60 OY9.2: 14 residues within 4Å: Chain A: I.44, L.48, F.49, S.52, Y.82 Chain B: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.48, B:L.23, B:E.26, B:Y.62, B:Y.62, B:L.114 pi-Stacking: A:Y.82 Hydrogen bonds: B:Y.62 OY9.3: 13 residues within 4Å: Chain B: I.44, L.48, F.49, S.52, T.79, Y.82 Chain C: R.22, E.26, I.28, H.60, Y.62, W.90, V.92 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:I.44, B:L.48, B:Y.82, B:Y.82, C:E.26, C:H.60 Hydrogen bonds: C:Y.62 OY9.4: 15 residues within 4Å: Chain C: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain D: R.22, L.23, E.26, H.60, Y.62, W.90, V.92, L.114 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.23, D:E.26, D:Y.62, D:V.92, D:L.114, C:L.48 Hydrogen bonds: C:Q.51 pi-Stacking: C:Y.82 OY9.5: 15 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, V.92 11 PLIP interactions: 6 interactions with chain D, 5 interactions with chain E Hydrophobic interactions: D:I.44, D:L.48, D:L.48, D:L.48, E:L.23, E:E.26, E:I.28, E:Y.62, E:Y.62 Hydrogen bonds: D:Q.51 pi-Stacking: D:Y.82 OY9.6: 15 residues within 4Å: Chain E: I.44, L.48, F.49, S.52, T.79, Y.82 Chain F: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 8 PLIP interactions: 5 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:L.23, F:E.26, F:H.60, F:Y.62, F:L.114, E:L.48, E:L.48 pi-Stacking: E:Y.82 OY9.7: 13 residues within 4Å: Chain F: L.48, F.49, Q.51, S.52, T.79, Y.82 Chain G: R.22, L.23, E.26, H.60, Y.62, W.90, V.92 6 PLIP interactions: 2 interactions with chain G, 4 interactions with chain F Hydrophobic interactions: G:L.23, G:E.26, F:L.48, F:L.48 Hydrogen bonds: F:Q.51 pi-Stacking: F:Y.82 OY9.8: 14 residues within 4Å: Chain H: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92 Chain N: I.44, L.48, F.49, S.52, T.79, Y.82 9 PLIP interactions: 5 interactions with chain H, 4 interactions with chain N Hydrophobic interactions: H:L.23, H:E.26, H:Y.62, H:Y.62, N:I.44, N:L.48, N:Y.82, N:Y.82 pi-Stacking: H:H.60 OY9.9: 14 residues within 4Å: Chain H: I.44, L.48, F.49, S.52, Y.82 Chain I: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 7 PLIP interactions: 2 interactions with chain H, 5 interactions with chain I Hydrophobic interactions: H:L.48, I:L.23, I:E.26, I:Y.62, I:Y.62, I:L.114 pi-Stacking: H:Y.82 OY9.10: 13 residues within 4Å: Chain I: I.44, L.48, F.49, S.52, T.79, Y.82 Chain J: R.22, E.26, I.28, H.60, Y.62, W.90, V.92 6 PLIP interactions: 2 interactions with chain J, 4 interactions with chain I Hydrophobic interactions: J:E.26, J:H.60, I:I.44, I:L.48, I:Y.82, I:Y.82 OY9.11: 15 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, H.60, Y.62, W.90, V.92, L.114 9 PLIP interactions: 3 interactions with chain J, 6 interactions with chain K Hydrophobic interactions: J:L.48, K:L.23, K:E.26, K:Y.62, K:V.92, K:L.114 Hydrogen bonds: J:Q.51, K:Y.62 pi-Stacking: J:Y.82 OY9.12: 15 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, I.28, H.60, Y.62, W.90, V.92 12 PLIP interactions: 6 interactions with chain L, 6 interactions with chain K Hydrophobic interactions: L:L.23, L:E.26, L:I.28, L:Y.62, L:Y.62, K:I.44, K:L.48, K:L.48, K:L.48 Hydrogen bonds: L:Y.62, K:Q.51 pi-Stacking: K:Y.82 OY9.13: 15 residues within 4Å: Chain L: I.44, L.48, F.49, S.52, T.79, Y.82 Chain M: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 9 PLIP interactions: 3 interactions with chain L, 6 interactions with chain M Hydrophobic interactions: L:L.48, L:L.48, M:L.23, M:E.26, M:H.60, M:Y.62, M:L.114 pi-Stacking: L:Y.82 Hydrogen bonds: M:Y.62 OY9.14: 13 residues within 4Å: Chain M: L.48, F.49, Q.51, S.52, T.79, Y.82 Chain N: R.22, L.23, E.26, H.60, Y.62, W.90, V.92 7 PLIP interactions: 4 interactions with chain M, 3 interactions with chain N Hydrophobic interactions: M:L.48, M:L.48, N:L.23, N:E.26 Hydrogen bonds: M:Q.51, N:Y.62 pi-Stacking: M:Y.82

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

Related Entries With Identical Sequence