SMTL ID : 7abr.1

Cryo-EM structure of B. subtilis ClpC (DWB mutant) hexamer bound to a substrate polypeptide

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: D.180, P.181, V.182, I.183, P.210, G.211, V.212, G.213, K.214, T.215, A.216, I.350, P.388, D.389, I.392 Chain F: R.332 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:D.180, A:I.183, A:I.183, A:G.211, A:V.212, A:G.213, A:K.214, A:T.215, A:T.215, A:T.215, A:A.216 Salt bridges: A:K.214, F:R.332, F:R.332 ADP.2: 13 residues within 4Å: Chain A: R.509, V.510, I.511, Q.513, T.547, G.548, V.549, G.550, K.551, T.552, E.553, I.722, M.726 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:I.511, A:Q.513, A:G.548, A:K.551, A:T.552, A:T.552, A:R.763 ADP.4: 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, L.714, I.722, A.762, R.763, R.766 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:I.511, B:I.511, B:G.548, B:G.550, B:K.551, B:T.552, B:T.552, B:T.552, B:E.553, B:R.763, B:R.766 Salt bridges: B:K.551, B:K.551, B:R.763, B:R.763 ADP.11: 15 residues within 4Å: Chain E: R.332 Chain F: D.180, V.182, I.183, R.185, P.210, G.211, V.212, G.213, K.214, T.215, A.216, L.354, P.388, I.392 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:D.180, F:I.183, F:I.183, F:G.211, F:V.212, F:G.213, F:K.214, F:T.215, F:T.215, F:A.216

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

ATP.3: 18 residues within 4Å: Chain A: R.306, A.329, R.332, R.333 Chain B: D.180, P.181, V.182, I.183, R.185, P.210, V.212, G.213, K.214, T.215, A.216, I.350, P.388, I.392 14 PLIP interactions: 6 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:R.306, B:D.180, B:D.180, B:I.183, B:I.183, B:G.213, B:K.214, B:T.215, B:A.216 Salt bridges: A:R.306, A:R.332, A:R.332, A:R.332, A:R.333 ATP.5: 18 residues within 4Å: Chain B: R.332, R.333 Chain C: D.180, P.181, V.182, I.183, R.185, P.210, G.211, V.212, G.213, K.214, T.215, A.216, I.350, L.354, P.388, I.392 15 PLIP interactions: 11 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:D.180, C:I.183, C:I.183, C:G.211, C:V.212, C:G.213, C:K.214, C:T.215, C:A.216 Salt bridges: C:K.214, C:K.214, B:R.332, B:R.332, B:R.332, B:R.333 ATP.6: 19 residues within 4Å: Chain B: E.635, R.704 Chain C: R.509, V.510, I.511, P.546, T.547, G.548, V.549, G.550, K.551, T.552, E.553, N.659, L.714, I.722, M.726, A.762, R.763 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:I.511, C:I.511, C:G.548, C:V.549, C:G.550, C:K.551, C:T.552, C:T.552, C:E.553, C:E.553, C:R.763, B:E.635 Salt bridges: C:K.551, C:K.551, C:K.551, C:R.763, C:R.763, B:R.704 ATP.7: 17 residues within 4Å: Chain C: R.332, R.333 Chain D: P.181, V.182, I.183, R.185, P.210, G.211, V.212, G.213, K.214, T.215, A.216, I.350, L.354, P.388, I.392 15 PLIP interactions: 11 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:I.183, D:I.183, D:G.211, D:V.212, D:K.214, D:T.215, D:T.215, D:T.215, D:A.216 Salt bridges: D:K.214, D:K.214, C:R.332, C:R.332, C:R.332, C:R.333 ATP.8: 19 residues within 4Å: Chain C: E.635, E.700, R.704 Chain D: R.509, V.510, I.511, T.547, G.548, V.549, G.550, K.551, T.552, E.553, N.659, L.714, M.726, G.761, A.762, R.763 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:I.511, D:I.511, D:T.547, D:V.549, D:G.550, D:T.552, D:T.552, D:E.553, D:E.553, D:N.659 Salt bridges: D:K.551, D:K.551, D:R.556, D:R.763, D:R.763, D:R.763, C:R.704 ATP.9: 15 residues within 4Å: Chain D: E.700, R.704 Chain E: V.510, I.511, T.547, G.548, V.549, G.550, K.551, T.552, E.553, I.722, M.726, A.762, R.763 17 PLIP interactions: 14 interactions with chain E, 3 interactions with chain D 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:E.553, D:E.700, D:E.700 Salt bridges: E:K.551, E:K.551, E:R.763, E:R.763, E:R.763, D:R.704 ATP.10: 17 residues within 4Å: Chain D: R.332, R.333 Chain E: P.181, V.182, I.183, R.185, P.210, G.211, V.212, G.213, K.214, T.215, A.216, I.350, L.354, P.388, I.392 13 PLIP interactions: 9 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:I.183, E:I.183, E:G.213, E:K.214, E:T.215, E:T.215, E:A.216 Salt bridges: E:K.214, E:K.214, D:R.332, D:R.332, D:R.332, D:R.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morreale, F.E. et al., BacPROTACs mediate targeted protein degradation in bacteria. Cell (2022)

Release Date

2021-10-06

Peptides

Negative regulator of genetic competence ClpC/MecB: ABCDEF
substrate polypeptide: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
S

Negative regulator of genetic competence ClpC/MecB

substrate polypeptide

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