SMTL ID : 9qqr.1

S.aureus ClpC decameric resting state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.70 Å

Oligo State

homo-10-mer

Ligands

9 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 11 residues within 4Å: Chain A: R.509, V.510, I.511, G.548, V.549, G.550, T.552, E.553, M.725, A.762, R.763 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:I.511, A:I.511, A:G.548, A:T.552, A:E.553, A:E.553 Salt bridges: A:R.763, A:R.763, A:R.763 ATP.2: 12 residues within 4Å: Chain A: N.703 Chain B: R.509, V.510, I.511, G.548, V.549, G.550, T.552, E.553, M.725, A.762, R.763 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:I.511, B:I.511, B:G.548, B:V.549, B:G.550, B:T.552, B:E.553, B:E.553 Salt bridges: B:R.763, B:R.763, B:R.763 ATP.4: 14 residues within 4Å: Chain C: R.509, V.510, I.511, G.548, V.549, G.550, K.551, T.552, E.553, I.722, M.725, A.762, R.763, I.766 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:I.511, C:I.511, C:G.548, C:V.549, C:K.551, C:T.552, C:T.552, C:E.553, C:E.553, C:E.553, C:D.617 Salt bridges: C:R.763, C:R.763, C:R.763 ATP.6: 17 residues within 4Å: Chain D: R.509, V.510, I.511, T.547, G.548, V.549, G.550, K.551, T.552, E.553, R.556, I.722, M.725, M.726, A.762, R.763, I.766 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:I.511, D:I.511, D:T.547, D:G.548, D:G.550, D:K.551, D:T.552, D:T.552, D:E.553, D:R.556 Salt bridges: D:R.763, D:R.763, D:R.763 ATP.8: 13 residues within 4Å: Chain D: N.703 Chain E: I.511, T.547, G.548, V.549, G.550, K.551, T.552, E.553, I.722, M.725, A.762, R.763 17 PLIP interactions: 16 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:I.511, E:I.511, E:T.547, E:G.548, E:V.549, E:G.550, E:K.551, E:T.552, E:T.552, E:T.552, E:E.553, E:E.553, E:E.553, D:N.703 Salt bridges: E:R.763, E:R.763, E:R.763 ATP.9: 15 residues within 4Å: Chain F: R.509, V.510, I.511, G.512, G.548, V.549, G.550, K.551, T.552, E.553, I.722, M.725, A.762, R.763, I.766 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:I.511, F:I.511, F:G.548, F:G.550, F:K.551, F:T.552, F:T.552, F:E.553, F:E.553, F:E.553 Salt bridges: F:R.763, F:R.763, F:R.763 ATP.10: 11 residues within 4Å: Chain G: V.510, I.511, G.548, V.549, G.550, T.552, E.553, I.722, A.762, R.763, I.766 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:I.511, G:I.511, G:G.548, G:G.550, G:T.552, G:T.552, G:E.553, G:E.553 Salt bridges: G:R.763, G:R.763, G:R.763 ATP.12: 14 residues within 4Å: Chain H: V.510, I.511, T.547, G.548, V.549, G.550, K.551, T.552, E.553, I.722, M.725, M.726, R.763, I.766 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:I.511, H:I.511, H:G.548, H:G.548, H:G.550, H:T.552, H:T.552, H:E.553 Salt bridges: H:R.763, H:R.763, H:R.763 ATP.14: 16 residues within 4Å: Chain H: N.703 Chain I: R.509, V.510, I.511, T.547, G.548, V.549, G.550, K.551, T.552, E.553, I.722, M.725, A.762, R.763, I.766 13 PLIP interactions: 12 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:I.511, I:I.511, I:G.548, I:G.548, I:G.550, I:T.552, I:T.552, I:E.553, I:E.553, H:N.703 Salt bridges: I:R.763, I:R.763, I:R.763

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 13 residues within 4Å: Chain A: A.328, R.332 Chain B: I.183, G.211, V.212, G.213, K.214, T.215, A.216, E.219, I.350, L.354, P.388 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.183, B:G.211, B:G.213, B:K.214, B:T.215, B:E.219 Salt bridges: B:K.214, A:R.332 ADP.5: 11 residues within 4Å: Chain B: R.332 Chain C: P.181, I.183, R.185, G.211, V.212, G.213, K.214, T.215, A.216, I.350 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:I.183, C:I.183, C:G.211, C:V.212, C:G.213, C:K.214, C:T.215, C:T.215 Salt bridges: B:R.332, B:R.332 ADP.7: 13 residues within 4Å: Chain C: R.332 Chain D: V.182, I.183, R.185, P.210, G.211, G.213, K.214, T.215, A.216, I.350, L.354, I.392 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:I.183, D:I.183, D:G.211, D:G.213, D:K.214, D:T.215, D:T.215, D:A.216 Salt bridges: D:K.214, C:R.332, C:R.332 ADP.11: 15 residues within 4Å: Chain F: R.332 Chain G: P.181, V.182, I.183, R.185, P.210, G.211, G.213, K.214, T.215, A.216, I.350, L.354, P.388, D.389 10 PLIP interactions: 8 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:I.183, G:I.183, G:G.211, G:G.213, G:K.214, G:T.215, G:T.215 Salt bridges: G:K.214, F:R.332, F:R.332 ADP.13: 14 residues within 4Å: Chain G: R.332 Chain H: D.180, P.181, V.182, I.183, R.185, G.211, G.213, K.214, T.215, A.216, I.350, L.354, P.388 9 PLIP interactions: 7 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:D.180, H:I.183, H:I.183, H:G.211, H:G.213, H:K.214, H:T.215 Salt bridges: G:R.332, G:R.332 ADP.15: 15 residues within 4Å: Chain H: A.328, R.332 Chain I: P.181, V.182, I.183, R.185, G.211, V.212, G.213, K.214, T.215, A.216, I.350, P.388, I.392 7 PLIP interactions: 6 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:I.183, I:R.185, I:G.211, I:G.213, I:K.214, I:T.215 Salt bridges: H:R.332

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jenne, T. et al., Allosteric control of the bacterial ClpC/ClpP protease and its hijacking by antibacterial peptide. To Be Published

Release Date

2025-07-30

Peptides

ATP-dependent Clp protease ATP-binding subunit ClpC: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
H

D
I

E
J

F
E

G
D

H
C

I
B

J
A

ATP-dependent Clp protease ATP-binding subunit ClpC

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