SMTL ID : 8e91.1

Cryo-EM structure of substrate-free ClpX.ClpP

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-14-mer

Ligands

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

AGS.1: 22 residues within 4Å: Chain A: Y.77, V.78, I.79, Q.81, P.120, T.121, G.122, S.123, G.124, K.125, T.126, L.127, D.184, A.250, L.317, I.325, P.329, A.369, R.370 Chain B: E.216, E.303, R.307 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:I.79, A:I.79, A:G.122, A:S.123, A:G.124, A:K.125, A:K.125, A:T.126, A:T.126, A:T.126, A:L.127, A:R.370, A:R.370, B:R.307, B:R.307 Salt bridges: A:K.125, A:R.370, A:R.370 AGS.2: 23 residues within 4Å: Chain B: Y.77, V.78, I.79, Q.81, P.120, T.121, G.122, S.123, G.124, K.125, T.126, L.127, E.185, A.250, L.317, I.325, P.329, A.369, R.370 Chain C: E.216, E.303, R.307 Ligands: MG.3 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:I.79, B:G.122, B:S.123, B:S.123, B:G.124, B:K.125, B:T.126, B:T.126, B:L.127, B:R.370, B:R.370, C:R.307, C:R.307 Salt bridges: B:K.125, B:R.370, B:R.370 AGS.4: 21 residues within 4Å: Chain C: Y.77, V.78, I.79, Q.81, T.121, G.122, S.123, G.124, K.125, T.126, L.127, E.185, A.250, L.317, I.325, P.329, A.369, R.370 Chain D: E.303, R.307 Ligands: MG.5 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:I.79, C:G.122, C:S.123, C:S.123, C:G.124, C:K.125, C:K.125, C:T.126, C:L.127, C:R.370, C:R.370, D:E.303, D:R.307, D:R.307 Salt bridges: C:K.125, C:R.370, C:R.370 AGS.6: 21 residues within 4Å: Chain D: Y.77, V.78, I.79, Q.81, T.121, G.122, S.123, G.124, K.125, T.126, L.127, E.185, A.250, L.317, I.325, P.329, A.369, R.370 Chain E: E.303, R.307 Ligands: MG.7 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:I.79, D:I.79, D:G.122, D:S.123, D:G.124, D:K.125, D:K.125, D:T.126, D:L.127, D:E.185, D:R.370, D:R.370, E:R.307, E:R.307 Salt bridges: D:K.125, D:R.370, D:R.370

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain B: K.125, T.126, D.184, E.185 Chain C: R.307 Ligands: AGS.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.126 MG.5: 7 residues within 4Å: Chain C: T.126, D.184, E.185, R.370 Chain D: E.216, R.307 Ligands: AGS.4 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.126 MG.7: 7 residues within 4Å: Chain D: T.126, D.184, E.185, R.370 Chain E: E.216, R.307 Ligands: AGS.6 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.126

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

ADP.8: 18 residues within 4Å: Chain E: Y.77, V.78, I.79, T.121, G.122, S.123, G.124, K.125, T.126, L.127, D.184, L.317, I.325, P.329, A.369, R.370 Chain F: E.303, R.307 11 PLIP interactions: 8 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:I.79, E:I.79, E:T.121, E:G.122, E:T.126, E:D.184, F:E.303, F:R.307 Salt bridges: E:K.125, E:R.370, F:R.307 ADP.9: 17 residues within 4Å: Chain F: Y.77, V.78, I.79, P.120, T.121, G.122, S.123, G.124, K.125, T.126, L.127, Y.182, L.317, I.325, P.329, A.369, R.370 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:I.79, F:I.79, F:G.122, F:S.123, F:S.123, F:S.123, F:G.124, F:K.125, F:T.126, F:T.126 Salt bridges: F:K.125, F:R.370

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghanbarpour, A. et al., Cryo-EM structure of substrate-free DNClpX.ClpP. Nat Commun (2023)

Release Date

2023-11-08

Peptides

ATP-dependent Clp protease ATP-binding subunit ClpX: ABCDEF
ATP-dependent Clp protease proteolytic subunit: GHIJKLMNOPQRST

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
H

H
I

I
J

J
K

K
L

L
M

M
N

N
h

O
i

P
j

Q
k

R
l

S
m

T
n

ATP-dependent Clp protease ATP-binding subunit ClpX

ATP-dependent Clp protease proteolytic subunit

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