SMTL ID : 6wrf.1

ClpX-ClpP complex bound to GFP-ssrA, recognition complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-7-1-mer

Ligands

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

AGS.1: 23 residues within 4Å: Chain A: Y.41, V.42, I.43, Q.45, P.84, T.85, G.86, S.87, G.88, K.89, T.90, L.91, E.149, A.214, L.281, I.289, P.293, A.333, R.334 Chain B: E.180, E.267, R.271 Ligands: MG.2 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:I.43, A:G.86, A:S.87, A:S.87, A:G.88, A:K.89, A:T.90, A:T.90, A:L.91, A:R.334, B:R.271, B:R.271 Salt bridges: A:K.89, A:R.334, A:R.334 AGS.3: 22 residues within 4Å: Chain B: Y.41, V.42, I.43, G.44, Q.45, T.85, G.86, S.87, G.88, K.89, T.90, L.91, E.149, A.214, L.281, I.289, P.293, A.333, R.334 Chain C: E.267, R.271 Ligands: MG.4 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:I.43, B:G.86, B:S.87, B:S.87, B:G.88, B:K.89, B:T.90, B:T.90, B:L.91, B:R.334, B:R.334, C:R.271 Salt bridges: B:K.89, B:R.334, B:R.334 AGS.5: 22 residues within 4Å: Chain C: Y.41, V.42, I.43, Q.45, T.85, G.86, S.87, G.88, K.89, T.90, L.91, E.149, A.214, L.281, I.289, P.293, A.333, R.334 Chain D: E.180, E.267, R.271 Ligands: MG.6 16 PLIP interactions: 14 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:I.43, C:I.43, C:G.86, C:S.87, C:G.88, C:K.89, C:T.90, C:T.90, C:L.91, C:R.334, C:R.334, D:R.271, D:R.271 Salt bridges: C:K.89, C:R.334, C:R.334 AGS.7: 22 residues within 4Å: Chain D: Y.41, V.42, I.43, G.44, Q.45, T.85, G.86, S.87, G.88, K.89, T.90, L.91, D.148, A.214, L.281, I.289, P.293, A.333, R.334 Chain E: E.267, R.271 Ligands: MG.8 17 PLIP interactions: 14 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:I.43, D:G.86, D:S.87, D:S.87, D:G.88, D:K.89, D:T.90, D:T.90, D:L.91, D:R.334, D:R.334, E:E.267, E:R.271, E:R.271 Salt bridges: D:K.89, D:R.334, D:R.334 AGS.10: 24 residues within 4Å: Chain A: E.180, E.267, R.271 Chain N: Y.41, V.42, I.43, Q.45, P.84, T.85, G.86, S.87, G.88, K.89, T.90, L.91, D.148, E.149, A.214, L.281, I.289, P.293, A.333, R.334 Ligands: MG.11 19 PLIP interactions: 15 interactions with chain N, 4 interactions with chain A Hydrogen bonds: N:I.43, N:I.43, N:G.86, N:S.87, N:S.87, N:G.88, N:K.89, N:K.89, N:T.90, N:L.91, N:R.334, N:R.334, A:E.267, A:E.267, A:R.271, A:R.271 Salt bridges: N:K.89, N:R.334, N:R.334

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: K.89, T.90, D.148 Chain B: R.271 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.90 MG.4: 4 residues within 4Å: Chain B: T.90, D.148, E.149 Ligands: AGS.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.90, B:D.148 MG.6: 4 residues within 4Å: Chain C: T.90, D.148, E.149 Ligands: AGS.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.90, C:D.148 MG.8: 6 residues within 4Å: Chain D: K.89, T.90, Y.146, D.148, E.149 Ligands: AGS.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.148, D:D.148 MG.11: 6 residues within 4Å: Chain N: K.89, T.90, Y.146, D.148, E.149 Ligands: AGS.10 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:T.90, N:D.148, N:D.148

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

ADP.9: 19 residues within 4Å: Chain E: Y.41, V.42, I.43, Q.45, P.84, T.85, G.86, S.87, G.88, K.89, T.90, L.91, Y.146, D.148, L.281, I.289, P.293, A.333, R.334 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:I.43, E:I.43, E:G.86, E:G.88, E:K.89, E:T.90, E:T.90 Salt bridges: E:K.89, E:K.89, E:R.334, E:R.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fei, X. et al., Structural basis of ClpXP recognition and unfolding of ssrA-tagged substrates. Elife (2020)

Release Date

2020-11-04

Peptides

ATP-dependent Clp protease ATP-binding subunit ClpX: ABCDEN
ATP-dependent Clp protease proteolytic subunit: FGHIJKL
Green fluorescent protein: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
E

E
F

N
A

F
H

G
I

H
J

I
K

J
L

K
M

L
N

M
S

ATP-dependent Clp protease ATP-binding subunit ClpX

ATP-dependent Clp protease proteolytic subunit

Green fluorescent protein

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