SMTL ID : 9qrw.1

S.aureus ClpC dodecameric resting state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.40 Å

Oligo State

homo-12-mer

Ligands

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

ATP.1: 15 residues within 4Å: Chain B: R.509, V.510, I.511, T.547, G.548, V.549, G.550, K.551, T.552, E.553, D.617, I.722, M.725, R.763 Chain C: N.703 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:I.511, B:I.511, B:G.548, B:V.549, B:G.550, B:K.551, B:T.552, B:T.552, B:T.552, B:E.553, B:D.617, B:R.763, C:N.703 Salt bridges: B:R.763, B:R.763 ATP.2: 13 residues within 4Å: Chain C: V.510, I.511, T.547, G.548, V.549, G.550, K.551, T.552, E.553, I.722, M.726, R.763, I.766 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:I.511, C:I.511, C:T.547, C:T.547, C:G.548, C:V.549, C:G.550, C:K.551, C:T.552, C:T.552, C:E.553, C:R.763 Salt bridges: C:R.763 ATP.4: 16 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, I.722, M.725, M.726, R.763, I.766 Chain E: N.703 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:I.511, D:I.511, D:G.548, D:G.548, D:G.550, D:T.552, D:T.552, D:E.553, E:N.703 Salt bridges: D:R.763, D:R.763, D:R.763 ATP.6: 15 residues within 4Å: Chain E: 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: 13 interactions with chain E Hydrogen bonds: E:I.511, E:I.511, E:G.548, E:V.549, E:G.550, E:K.551, E:T.552, E:T.552, E:T.552, E:E.553 Salt bridges: E:R.763, E:R.763, E:R.763 ATP.10: 14 residues within 4Å: Chain G: R.509, I.511, T.547, G.548, V.549, G.550, K.551, T.552, E.553, R.571, I.722, A.762, R.763 Chain H: N.703 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:I.511, G:I.511, G:G.548, G:T.552, G:R.571 Salt bridges: G:R.763, G:R.763 ATP.11: 16 residues within 4Å: Chain H: R.509, V.510, I.511, T.547, G.548, V.549, G.550, K.551, T.552, E.553, R.571, D.617, I.722, M.725, R.763 Chain I: N.703 17 PLIP interactions: 16 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:I.511, H:I.511, H:T.547, H:G.548, H:V.549, H:G.550, H:K.551, H:T.552, H:T.552, H:T.552, H:E.553, H:E.553, H:R.571, H:D.617, I:N.703 Salt bridges: H:R.763, H:R.763 ATP.13: 15 residues within 4Å: 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 Chain J: N.703 14 PLIP interactions: 13 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:I.511, I:I.511, I:T.547, I:G.548, I:V.549, I:G.550, I:K.551, I:T.552, I:T.552, I:T.552, I:E.553, J:N.703 Salt bridges: I:R.763, I:R.763 ATP.15: 15 residues within 4Å: Chain J: 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 Chain K: N.703 13 PLIP interactions: 12 interactions with chain J, 1 interactions with chain K Hydrogen bonds: J:I.511, J:I.511, J:T.547, J:G.548, J:G.550, J:K.551, J:T.552, J:T.552, J:E.553, J:E.553, K:N.703 Salt bridges: J:R.763, J:R.763

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

ADP.3: 14 residues within 4Å: Chain C: V.182, I.183, R.185, E.209, P.210, G.211, V.212, G.213, K.214, T.215, A.216, I.350, P.388 Chain D: R.332 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:I.183, C:E.209, C:G.211, C:V.212, C:G.213, C:K.214, C:T.215, C:T.215, C:A.216 Salt bridges: C:K.214, D:R.332 ADP.5: 15 residues within 4Å: Chain D: V.182, I.183, R.185, E.209, P.210, G.211, V.212, G.213, K.214, T.215, A.216, I.350, P.388, I.392 Chain E: R.332 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:I.183, D:I.183, D:E.209, D:G.211, D:V.212, D:G.213, D:K.214, D:T.215, D:T.215, D:A.216, E:R.332 Salt bridges: D:K.214 ADP.7: 14 residues within 4Å: Chain E: V.182, I.183, G.184, R.185, P.210, G.211, V.212, G.213, K.214, T.215, A.216, I.350, P.388 Chain F: R.332 13 PLIP interactions: 10 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:I.183, E:R.185, E:E.209, E:G.211, E:V.212, E:G.213, E:K.214, E:T.215, E:T.215, E:A.216, F:R.332 Salt bridges: F:R.332, F:R.332 ADP.8: 14 residues within 4Å: Chain F: V.510, I.511, G.512, Q.513, T.547, G.548, V.549, G.550, K.551, T.552, E.553, L.714, I.722, I.766 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:G.512, F:T.547, F:G.548, F:G.550, F:T.552, F:T.552, F:T.552, F:E.553 ADP.9: 14 residues within 4Å: Chain F: P.181, V.182, I.183, R.185, G.211, V.212, G.213, K.214, T.215, A.216, E.219, I.350, P.388, D.389 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:I.183, F:I.183, F:R.185, F:G.211, F:G.213, F:K.214, F:T.215, F:E.219 ADP.12: 12 residues within 4Å: Chain H: I.183, R.185, G.211, V.212, G.213, K.214, T.215, A.216, I.350, P.388 Chain I: A.328, R.332 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:I.183, H:I.183, H:G.211, H:V.212, H:G.213, H:K.214, H:T.215, H:T.215, H:T.215 Salt bridges: H:K.214, I:R.332 ADP.14: 12 residues within 4Å: Chain I: I.183, R.185, P.210, G.211, V.212, G.213, K.214, T.215, A.216, I.350, P.388 Chain J: R.332 9 PLIP interactions: 7 interactions with chain I, 2 interactions with chain J Hydrogen bonds: I:R.185, I:G.211, I:V.212, I:G.213, I:K.214, I:T.215, I:T.215, J:R.332 Salt bridges: J:R.332 ADP.16: 13 residues within 4Å: Chain J: V.182, I.183, R.185, P.210, G.211, V.212, G.213, K.214, T.215, A.216, I.350, I.392 Chain K: R.332 11 PLIP interactions: 9 interactions with chain J, 2 interactions with chain K Hydrogen bonds: J:I.183, J:I.183, J:R.185, J:G.211, J:V.212, J:G.213, J:K.214, J:T.215, J:A.216 Salt bridges: K:R.332, K:R.332 ADP.17: 11 residues within 4Å: Chain K: T.547, G.548, V.549, G.550, K.551, T.552, E.553, M.725, A.762, R.763, I.766 8 PLIP interactions: 8 interactions with chain K Hydrogen bonds: K:T.547, K:T.547, K:G.548, K:V.549, K:K.551, K:T.552, K:E.553, K:E.553

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 peptides. To Be Published

Release Date

2025-07-30

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
N

B
M

C
L

D
K

E
J

F
I

G
C

H
D

I
E

J
F

K
G

L
B

ATP-dependent Clp protease ATP-binding subunit ClpC

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