SMTL ID : 6h23.1

Crystal structure of the hClpP Y118A mutant with an activating small molecule

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.09 Å

Oligo State

homo-14-mer

Ligands

14 x FJT: ~{N}-(1,3-benzodioxol-5-ylmethyl)-5-[(2-chloranyl-4-fluoranyl-phenyl)methyl]-1,3,4-oxadiazole-2-carboxamide(Non-covalent)

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

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: Q.138, A.139 Chain H: Q.123, K.146 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.138, A:A.139 EDO.7: 6 residues within 4Å: Chain E: V.70, Q.123, I.142, K.146 Chain K: Q.138, A.139 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:Q.138, K:A.139 EDO.9: 3 residues within 4Å: Chain F: Q.123, I.142, K.146 No protein-ligand interaction detected (PLIP) EDO.18: 5 residues within 4Å: Chain N: V.70, Q.123, I.142, K.146, L.149 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stahl, M. et al., Selective Activation of Human Caseinolytic Protease P (ClpP). Angew. Chem. Int. Ed. Engl. (2018)

Release Date

2018-08-29

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