SMTL ID : 6nb1.1

Crystal structure of Escherichia coli ClpP protease complexed with small molecule activator, ACP1-06

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-14-mer

Ligands

14 x KHS: N-{2-[(2-chlorophenyl)sulfanyl]ethyl}-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]sulfonyl}propanamide(Non-covalent)

KHS.1: 14 residues within 4Å: Chain A: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, F.126, L.203, R.206 Chain G: L.62, F.63, A.66, F.96 7 PLIP interactions: 1 interactions with chain G, 6 interactions with chain A Hydrophobic interactions: G:A.66, A:E.40, A:Y.74, A:Y.74, A:Y.76, A:L.203 Hydrogen bonds: A:R.206 KHS.3: 13 residues within 4Å: Chain A: L.62, F.63, A.66, F.96 Chain B: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, F.126, R.206 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:E.40, B:Y.74, B:Y.74, B:Y.76, B:I.104, A:A.66 Hydrogen bonds: B:E.40, B:E.40 KHS.5: 11 residues within 4Å: Chain B: L.62, F.63, A.66, F.96 Chain C: L.37, E.40, V.42, Y.74, Y.76, F.126, R.206 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:A.66, C:E.40, C:V.42, C:Y.74, C:Y.74, C:Y.74, C:Y.76 Hydrogen bonds: C:Y.76, C:R.206 KHS.7: 14 residues within 4Å: Chain C: L.62, F.63, A.66, F.96 Chain D: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, F.126, L.203, R.206 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:A.66, D:Y.74, D:Y.74, D:Y.74, D:Y.76, D:L.203 Hydrogen bonds: D:Y.76, D:R.206 KHS.9: 13 residues within 4Å: Chain D: L.62, F.63, A.66 Chain E: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, F.126, L.203, R.206 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain E Hydrophobic interactions: D:A.66, E:E.40, E:Y.74, E:Y.74, E:Y.76, E:L.203 Hydrogen bonds: E:Y.76 KHS.11: 13 residues within 4Å: Chain E: L.62, F.63, A.66, F.96 Chain F: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, F.126, R.206 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:E.40, F:Y.74, F:Y.74, F:Y.74, F:Y.76, E:A.66 Hydrogen bonds: F:Y.76, F:R.206 KHS.13: 13 residues within 4Å: Chain F: L.62, F.63, A.66, F.96 Chain G: R.36, L.37, E.40, V.42, Y.74, Y.76, F.126, L.203, R.206 6 PLIP interactions: 5 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:E.40, G:Y.74, G:Y.74, G:Y.76, F:A.66 Hydrogen bonds: G:R.206 KHS.15: 14 residues within 4Å: Chain H: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, F.126, L.203, R.206 Chain I: L.62, F.63, A.66, F.96 8 PLIP interactions: 7 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: H:E.40, H:Y.74, H:Y.74, H:Y.76, H:L.203, I:A.66 Hydrogen bonds: H:Y.76, H:R.206 KHS.17: 13 residues within 4Å: Chain I: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, F.126, R.206 Chain J: L.62, F.63, A.66, F.96 7 PLIP interactions: 6 interactions with chain I, 1 interactions with chain J Hydrophobic interactions: I:E.40, I:Y.74, I:Y.74, I:Y.76, J:A.66 Hydrogen bonds: I:Y.76, I:R.206 KHS.19: 13 residues within 4Å: Chain J: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, F.126, R.206 Chain K: L.62, F.63, A.66, F.96 5 PLIP interactions: 4 interactions with chain J, 1 interactions with chain K Hydrophobic interactions: J:Y.74, J:Y.74, J:Y.76, K:A.66 Hydrogen bonds: J:R.206 KHS.21: 14 residues within 4Å: Chain K: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, F.126, L.203, R.206 Chain L: L.62, F.63, A.66, F.96 6 PLIP interactions: 5 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: K:Y.74, K:Y.74, K:Y.76, K:I.104, K:L.203, L:A.66 KHS.23: 14 residues within 4Å: Chain L: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, F.126, L.203, R.206 Chain M: L.62, F.63, A.66, F.96 8 PLIP interactions: 7 interactions with chain L, 1 interactions with chain M Hydrophobic interactions: L:E.40, L:Y.74, L:Y.74, L:Y.76, L:I.104, L:L.203, M:A.66 Hydrogen bonds: L:R.206 KHS.25: 14 residues within 4Å: Chain M: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, F.126, L.203, R.206 Chain N: L.62, F.63, A.66, F.96 7 PLIP interactions: 6 interactions with chain M, 1 interactions with chain N Hydrophobic interactions: M:E.40, M:Y.74, M:Y.74, M:Y.76, M:L.203, N:A.66 Hydrogen bonds: M:R.206 KHS.27: 13 residues within 4Å: Chain H: L.62, F.63, A.66, F.96 Chain N: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, F.126, R.206 8 PLIP interactions: 7 interactions with chain N, 1 interactions with chain H Hydrophobic interactions: N:E.40, N:Y.74, N:Y.74, N:Y.74, N:Y.76, H:A.66 Hydrogen bonds: N:Y.76, N:R.206

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: E.155, K.158, V.159 Chain B: R.132, F.187, L.188, S.189 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:A.190 Hydrogen bonds: A:K.158 GOL.4: 7 residues within 4Å: Chain B: E.155, K.158, V.159, R.162 Chain C: R.132, L.188, S.189 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.162, B:R.162 GOL.6: 6 residues within 4Å: Chain C: E.155, K.158, V.159 Chain D: R.132, F.187, S.189 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Water bridges: D:S.189, C:E.155 Hydrogen bonds: C:E.155 GOL.8: 6 residues within 4Å: Chain D: E.155, K.158, V.159 Chain E: R.132, L.188, S.189 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:E.155, E:R.132 Water bridges: D:E.155, E:S.189 GOL.10: 7 residues within 4Å: Chain E: E.155, K.158, V.159 Chain F: R.132, F.187, L.188, S.189 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain E Water bridges: F:S.131, F:F.187, F:S.189, F:A.190, E:E.155 GOL.12: 6 residues within 4Å: Chain F: E.155, K.158, V.159 Chain G: R.132, L.188, S.189 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:R.132, F:E.155 Water bridges: G:S.189, F:K.158 GOL.14: 7 residues within 4Å: Chain A: R.132, L.188, S.189 Chain G: E.155, K.158, V.159, R.162 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:R.162 Water bridges: G:E.155, G:K.158, G:R.162 GOL.16: 6 residues within 4Å: Chain H: E.155, K.158, R.162 Chain N: R.132, L.188, S.189 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:R.162 Water bridges: H:E.155, H:K.158 GOL.18: 6 residues within 4Å: Chain H: R.132, L.188, S.189 Chain I: E.155, K.158, V.159 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain H Water bridges: I:E.155, I:E.155 Hydrogen bonds: H:R.132 GOL.20: 5 residues within 4Å: Chain I: R.132, S.189 Chain J: E.155, K.158, V.159 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:E.155, J:K.158 GOL.22: 6 residues within 4Å: Chain J: R.132, L.188, S.189 Chain K: E.155, K.158, V.159 3 PLIP interactions: 1 interactions with chain K, 2 interactions with chain J Hydrogen bonds: K:E.155 Water bridges: J:S.189, J:S.189 GOL.24: 6 residues within 4Å: Chain K: R.132, L.188, S.189 Chain L: E.155, K.158, V.159 4 PLIP interactions: 1 interactions with chain K, 3 interactions with chain L Water bridges: K:F.187, L:E.155, L:K.158, L:K.158 GOL.26: 6 residues within 4Å: Chain L: R.132, L.188, S.189 Chain M: E.155, K.158, V.159 2 PLIP interactions: 2 interactions with chain M Water bridges: M:E.155, M:K.158 GOL.28: 6 residues within 4Å: Chain M: R.132, L.188, S.189 Chain N: E.155, K.158, V.159 4 PLIP interactions: 2 interactions with chain N, 2 interactions with chain M Hydrogen bonds: N:K.158 Water bridges: N:E.155, M:S.189, M:S.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mabanglo, M.F. et al., ClpP protease activation results from the reorganization of the electrostatic interaction networks at the entrance pores. Commun Biol (2019)

Release Date

2019-11-13

Peptides

ATP-dependent Clp protease proteolytic subunit: 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

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