SMTL ID : 9gi1.1

Structure of the S.aureus MecA/ClpC/ClpP degradation system

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-14-1-6-mer

Ligands

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

ADP.1: 16 residues within 4Å: Chain P: P.181, V.182, I.183, R.185, P.210, G.211, V.212, G.213, K.214, T.215, A.216, D.279, L.354, P.388, D.389 Chain U: R.332 11 PLIP interactions: 9 interactions with chain P, 2 interactions with chain U Hydrogen bonds: P:I.183, P:I.183, P:G.211, P:G.213, P:K.214, P:T.215, P:A.216, P:D.279 Salt bridges: P:K.214, U:R.332, U:R.332 ADP.3: 17 residues within 4Å: Chain Q: R.509, V.510, I.511, 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, I.766 15 PLIP interactions: 15 interactions with chain Q Hydrogen bonds: Q:I.511, Q:I.511, Q:G.548, Q:V.549, Q:G.550, Q:K.551, Q:T.552, Q:T.552, Q:E.553, Q:E.553, Q:E.553, Q:N.659 Salt bridges: Q:K.551, Q:K.551, Q:R.763 ADP.13: 18 residues within 4Å: Chain S: R.332, R.333 Chain T: P.181, V.182, I.183, R.185, P.210, G.211, V.212, G.213, K.214, T.215, A.216, E.280, I.350, P.388, I.392 Ligands: MG.16 13 PLIP interactions: 3 interactions with chain S, 10 interactions with chain T Salt bridges: S:R.332, S:R.332, S:R.333, T:K.214, T:K.214 Hydrogen bonds: T:I.183, T:I.183, T:G.211, T:G.213, T:K.214, T:T.215, T:A.216, T:E.280 ADP.17: 14 residues within 4Å: Chain T: R.704 Chain U: R.509, V.510, I.511, G.548, V.549, G.550, K.551, T.552, E.553, L.714, I.722, A.762, R.763 12 PLIP interactions: 11 interactions with chain U, 1 interactions with chain T Hydrogen bonds: U:I.511, U:I.511, U:G.548, U:G.550, U:T.552, U:E.553, U:E.553, U:E.553 Salt bridges: U:K.551, U:K.551, U:R.763, T:R.704

6 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.2: 17 residues within 4Å: Chain P: R.332 Chain Q: P.181, V.182, I.183, R.185, E.209, G.211, V.212, G.213, K.214, T.215, A.216, E.280, I.350, L.354, I.392 Ligands: MG.4 15 PLIP interactions: 2 interactions with chain P, 13 interactions with chain Q Salt bridges: P:R.332, P:R.332, Q:K.214 Hydrogen bonds: Q:I.183, Q:R.185, Q:G.211, Q:V.212, Q:G.213, Q:K.214, Q:K.214, Q:T.215, Q:T.215, Q:T.215, Q:A.216, Q:E.280 AGS.5: 20 residues within 4Å: Chain Q: R.306, A.329, R.332, R.333 Chain R: P.181, V.182, I.183, R.185, P.210, G.211, V.212, G.213, K.214, T.215, A.216, E.280, I.350, L.354, I.392 Ligands: MG.7 13 PLIP interactions: 4 interactions with chain Q, 9 interactions with chain R Hydrogen bonds: Q:R.333, R:I.183, R:I.183, R:G.211, R:G.213, R:K.214, R:K.214, R:T.215, R:A.216 Salt bridges: Q:R.306, Q:R.332, Q:R.332, R:K.214 AGS.6: 21 residues within 4Å: Chain Q: D.635, E.700, R.704 Chain R: R.509, V.510, I.511, P.546, T.547, G.548, V.549, G.550, K.551, T.552, E.553, L.714, I.722, M.726, A.762, R.763, I.766 Ligands: MG.8 15 PLIP interactions: 14 interactions with chain R, 1 interactions with chain Q Hydrogen bonds: R:I.511, R:I.511, R:G.548, R:V.549, R:G.550, R:K.551, R:T.552, R:T.552, R:T.552, R:E.553, R:E.553, Q:R.704 Salt bridges: R:K.551, R:R.763, R:R.763 AGS.9: 20 residues within 4Å: Chain R: R.306, A.329, R.332, R.333 Chain S: P.181, V.182, I.183, R.185, E.209, G.211, V.212, G.213, K.214, T.215, A.216, E.280, I.350, L.354, I.392 Ligands: MG.11 15 PLIP interactions: 3 interactions with chain R, 12 interactions with chain S Hydrogen bonds: R:R.333, S:I.183, S:I.183, S:G.211, S:V.212, S:G.213, S:K.214, S:K.214, S:T.215, S:T.215, S:A.216, S:E.280 Salt bridges: R:R.332, R:R.332, S:K.214 AGS.10: 22 residues within 4Å: Chain R: R.704 Chain S: R.509, V.510, I.511, T.547, G.548, V.549, G.550, K.551, T.552, E.553, D.617, E.618, T.657, N.659, L.714, I.722, M.726, A.762, R.763, I.766 Ligands: MG.12 20 PLIP interactions: 2 interactions with chain R, 18 interactions with chain S Hydrogen bonds: R:R.704, R:R.704, S:I.511, S:I.511, S:G.548, S:V.549, S:G.550, S:K.551, S:K.551, S:T.552, S:T.552, S:T.552, S:E.553, S:E.553, S:E.618, S:T.657, S:T.657 Salt bridges: S:K.551, S:R.763, S:R.763 AGS.14: 19 residues within 4Å: Chain S: D.635, R.704 Chain T: R.509, V.510, I.511, T.547, G.548, V.549, G.550, K.551, T.552, E.553, D.617, L.714, I.722, M.726, A.762, R.763 Ligands: MG.15 16 PLIP interactions: 15 interactions with chain T, 1 interactions with chain S Hydrogen bonds: T:I.511, T:I.511, T:G.548, T:V.549, T:G.550, T:K.551, T:K.551, T:T.552, T:T.552, T:T.552, T:E.553, T:E.553, S:R.704 Salt bridges: T:K.551, T:R.763, T:R.763

7 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain Q: T.215, D.279, E.280 Ligands: AGS.2 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:T.215, Q:D.279, Q:D.279, Q:E.280 MG.7: 4 residues within 4Å: Chain R: T.215, D.279, E.280 Ligands: AGS.5 3 PLIP interactions: 3 interactions with chain R Metal complexes: R:T.215, R:D.279, R:D.279 MG.8: 3 residues within 4Å: Chain Q: D.635 Chain R: R.763 Ligands: AGS.6 2 PLIP interactions: 2 interactions with chain Q Metal complexes: Q:D.635, Q:D.635 MG.11: 4 residues within 4Å: Chain S: T.215, D.279, E.280 Ligands: AGS.9 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:T.215, S:D.279, S:D.279, S:E.280 MG.12: 5 residues within 4Å: Chain S: T.552, D.617, E.618, T.657 Ligands: AGS.10 5 PLIP interactions: 5 interactions with chain S Metal complexes: S:T.552, S:D.617, S:E.618, S:E.618, S:T.657 MG.15: 4 residues within 4Å: Chain T: T.552, D.617, T.657 Ligands: AGS.14 3 PLIP interactions: 3 interactions with chain T Metal complexes: T:T.552, T:D.617, T:D.617 MG.16: 4 residues within 4Å: Chain T: T.215, D.279, E.280 Ligands: ADP.13 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:T.215, T:D.279, T:D.279, T:E.280

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Azinas, S. et al., ClpC and ClpP act as reciprocal allosteric activators to form a highly efficient AAA+ protease. To Be Published

Release Date

2025-08-20

Peptides

ATP-dependent Clp protease proteolytic subunit: ABCDEFGHIJKLMN
Unidentified substrate of the MecA-ClpC-ClpP complex from S.aureus: O
ATP-dependent Clp protease ATP-binding subunit ClpC: PQRSTU

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Pa

B
Pb

C
Pc

D
Pd

E
Pe

F
Pf

G
Pg

H
Ph

I
Pi

J
Pl

K
Pm

L
Pn

M
Po

N
Pq

O
S

P
a

Q
b

R
c

S
d

T
e

U
f

ATP-dependent Clp protease proteolytic subunit

Unidentified substrate of the MecA-ClpC-ClpP complex from S.aureus

ATP-dependent Clp protease ATP-binding subunit ClpC

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