SMTL ID : 9pio.1

Cryo-EM structure of the ClpXP AAA+ protease bound to lambdaO-tagged Arc in a recognition complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.61 Å

Oligo State

hetero-6-1-14-mer

Ligands

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

AGS.1: 20 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, I.325, A.369, R.370 Chain C: E.216, E.303, R.307 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:I.79, B:Q.81, B:G.122, B:S.123, B:S.123, B:G.124, B:K.125, B:T.126, B:T.126, B:T.126, B:L.127, B:E.185, B:E.185, C:E.216 Salt bridges: B:K.125, B:R.370, B:R.370 AGS.3: 20 residues within 4Å: Chain C: 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 D: E.303, R.307 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:I.79, C:Q.81, C:G.122, C:S.123, C:S.123, C:G.124, C:K.125, C:T.126, C:T.126, C:T.126, C:L.127, C:E.185, C:E.185, D:R.307, D:R.307 Salt bridges: C:K.125, C:R.370, C:R.370 AGS.5: 24 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, R.373 Chain E: L.212, E.216, E.303, R.307 Ligands: MG.6 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:I.79, D:G.122, D:S.123, D:S.123, D:G.124, D:K.125, D:K.125, D:T.126, D:T.126, D:L.127, D:E.185 Salt bridges: D:K.125, D:R.370, D:R.370 AGS.7: 25 residues within 4Å: Chain E: 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, E.185, A.250, L.317, I.325, P.329, A.369, R.370 Chain F: L.212, E.216, E.303, R.307 Ligands: MG.8 17 PLIP interactions: 14 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:I.79, E:G.122, E:S.123, E:S.123, E:G.124, E:K.125, E:K.125, E:T.126, E:L.127, E:E.185, E:E.185, F:R.307, F:R.307 Salt bridges: E:K.125, E:R.370, E:R.370, F:R.307 AGS.9: 17 residues within 4Å: Chain F: Y.77, V.78, I.79, Q.81, P.120, T.121, G.122, S.123, G.124, K.125, T.126, L.127, A.250, I.325, P.329, A.369, R.370 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:I.79, F:T.121, F:G.122, F:S.123, F:S.123, F:G.124, F:K.125, F:K.125, F:T.126, F:T.126, F:L.127, F:R.370 Salt bridges: F:K.125

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain B: T.126, Y.182, D.184 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.184 MG.4: 4 residues within 4Å: Chain D: K.213, E.216, G.217, T.218 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.216 MG.6: 6 residues within 4Å: Chain D: T.126, D.184, R.370 Chain E: E.216, R.307 Ligands: AGS.5 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.126 MG.8: 6 residues within 4Å: Chain E: T.126, D.184, R.370 Chain F: E.216, R.307 Ligands: AGS.7 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Metal complexes: F:E.216, E:T.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghanbarpour, A. et al., Cryo-EM structure of substrate-free full-length ClpX.ClpP complex. To Be Published

Release Date

2025-11-12

Peptides

ATP-dependent Clp protease ATP-binding subunit ClpX: ABCDEF
Arc family DNA-binding protein: G
ATP-dependent Clp protease proteolytic subunit: HIJKLMNOPQRSTU

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

ATP-dependent Clp protease ATP-binding subunit ClpX

Arc family DNA-binding protein

ATP-dependent Clp protease proteolytic subunit

Related Entries With Identical Sequence