SMTL ID : 6pod.1

ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-7-1-mer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: Y.16, V.17, I.18, P.59, T.60, G.61, S.62, G.63, K.64, T.65, L.66, I.264, P.268, N.270, A.308, R.309 Chain B: E.242 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:I.18, A:I.18, A:G.61, A:S.62, A:G.63, A:K.64, A:T.65, A:T.65 Salt bridges: A:K.64, A:K.64, A:R.309, A:R.309

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

AGS.2: 22 residues within 4Å: Chain B: Y.16, V.17, I.18, Q.20, P.59, T.60, G.61, S.62, G.63, K.64, T.65, L.66, D.123, Q.124, A.189, I.264, P.268, A.308, R.309 Chain C: E.155, E.242, R.246 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:I.18, B:I.18, B:G.61, B:S.62, B:G.63, B:K.64, B:K.64, B:T.65, B:T.65, B:T.65, B:L.66, B:D.123, B:Q.124, C:R.246 Salt bridges: B:K.64, B:R.309, B:R.309 AGS.3: 22 residues within 4Å: Chain C: Y.16, V.17, I.18, Q.20, P.59, T.60, G.61, S.62, G.63, K.64, T.65, L.66, D.123, Q.124, A.189, I.264, P.268, A.308, R.309, R.312 Chain D: E.242, R.246 18 PLIP interactions: 15 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:I.18, C:I.18, C:G.61, C:S.62, C:G.63, C:K.64, C:T.65, C:T.65, C:T.65, C:L.66, C:D.123, C:Q.124, D:E.242, D:E.242, D:R.246 Salt bridges: C:K.64, C:R.309, C:R.309 AGS.4: 21 residues within 4Å: Chain D: Y.16, V.17, I.18, Q.20, P.59, T.60, G.61, S.62, G.63, K.64, T.65, L.66, A.189, I.264, P.268, A.308, R.309, R.312 Chain E: E.155, E.242, R.246 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:I.18, D:I.18, D:G.61, D:S.62, D:G.63, D:K.64, D:K.64, D:T.65, D:T.65, D:T.65, D:L.66, D:D.123, D:R.309, E:R.246 Salt bridges: D:K.64, D:R.309, D:R.309 AGS.5: 21 residues within 4Å: Chain E: Y.16, V.17, I.18, Q.20, P.59, T.60, G.61, S.62, G.63, K.64, T.65, L.66, D.123, A.189, I.264, P.268, A.308, R.309 Chain F: E.155, E.242, R.246 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:I.18, E:I.18, E:G.61, E:S.62, E:G.63, E:K.64, E:T.65, E:T.65, E:T.65, E:L.66, E:D.123, F:E.242, F:R.246 Salt bridges: E:K.64, E:R.309, E:R.309 AGS.6: 17 residues within 4Å: Chain F: Y.16, V.17, I.18, P.59, T.60, G.61, S.62, G.63, K.64, T.65, L.66, M.81, Y.121, I.264, P.268, A.308, R.309 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:I.18, F:G.61, F:S.62, F:G.63, F:K.64, F:K.64, F:T.65, F:T.65, F:T.65, F:L.66, F:A.308, F:R.309 Salt bridges: F:K.64, F:R.309, F:R.309

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fei, X. et al., Structures of the ATP-fueled ClpXP proteolytic machine bound to protein substrate. Elife (2020)

Release Date

2020-03-11

Peptides

ATP-dependent Clp protease ATP-binding subunit ClpX: ABCDEF
ATP-dependent Clp protease proteolytic subunit: GHIJKLM
substrate peptide: N

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
S

ATP-dependent Clp protease ATP-binding subunit ClpX

ATP-dependent Clp protease proteolytic subunit

substrate peptide

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