SMTL ID : 6wsg.1

ClpX-ClpP complex bound to ssrA-tagged GFP, intermediate 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 B: 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 C: E.180, E.267, R.271 Ligands: MG.2 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:I.43, B:G.86, 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, C:R.271 Salt bridges: B:K.89, B:R.334, B:R.334 AGS.3: 23 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, D.148, E.149, A.214, L.281, I.289, P.293, A.333, R.334 Chain D: E.180, E.267, R.271 Ligands: MG.4 16 PLIP interactions: 14 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:I.43, C:G.86, C:S.87, 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.5: 24 residues within 4Å: Chain D: 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 E: L.176, E.180, E.267, R.271 Ligands: MG.6 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:I.43, D:G.86, D:S.87, D:S.87, D:G.88, D:K.89, D:K.89, D:T.90, D:T.90, D:L.91, D:A.214 Salt bridges: D:K.89, D:R.334, D:R.334 AGS.7: 22 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, A.214, L.281, I.289, P.293, A.333, R.334 Chain F: E.180, E.267, R.271 Ligands: MG.8 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:I.43, E:G.86, E:S.87, E:S.87, E:G.88, E:K.89, E:T.90, E:T.90, E:L.91, E:R.334, E:R.334, F:R.271, F:R.271 Salt bridges: E:K.89, E:R.334, E:R.334 AGS.9: 20 residues within 4Å: Chain F: Y.41, V.42, I.43, G.44, Q.45, P.84, 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 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:I.43, F:G.86, F:S.87, F:G.88, F:K.89, F:K.89, F:T.90, F:T.90, F:L.91, F:D.148 Salt bridges: F:K.89

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain B: K.89, T.90, D.148, E.149 Chain C: K.177 Ligands: AGS.1 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.90, B:D.148 MG.4: 5 residues within 4Å: Chain C: T.90, D.148, E.149 Chain D: E.180 Ligands: AGS.3 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.90, C:D.148 MG.6: 4 residues within 4Å: Chain D: T.90, D.148, E.149 Ligands: AGS.5 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.90, D:D.148 MG.8: 4 residues within 4Å: Chain E: T.90, D.148 Chain F: E.180 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.90

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: ABCDEF
ATP-dependent Clp protease proteolytic subunit: GHIJKLM
Green fluorescent protein, + ssrA tag: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
L

H
K

I
J

J
I

K
H

L
N

M
M

N
S

ATP-dependent Clp protease ATP-binding subunit ClpX

ATP-dependent Clp protease proteolytic subunit

Green fluorescent protein, + ssrA tag

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