SMTL ID : 6pos.1

ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-7-mer

Ligands

1 x UNK- UNK- UNK- UNK- ARG- UNK- UNK- UNK: substrate peptide(Non-covalent)

UNK-UNK-UNK-UNK-ARG-UNK-UNK-UNK.1: 23 residues within 4Å: Chain A: K.131, T.138, R.139, D.140 Chain B: Y.92, V.93, T.138, R.139, V.141 Chain C: G.91, Y.92, V.93, V.141 Chain D: G.91, Y.92, V.93 Chain E: Y.92, V.93, R.139, V.141 Chain F: G.91, Y.92, V.93 8 PLIP interactions: 2 interactions with chain A, 2 interactions with chain F, 1 interactions with chain E, 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: A:K.131, A:T.138 Hydrophobic interactions: F:Y.92, F:V.93, E:V.141, B:V.93, D:Y.92, C:Y.92

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

AGS.2: 16 residues within 4Å: Chain A: Y.16, V.17, I.18, T.60, G.61, S.62, G.63, K.64, T.65, L.66, Q.124, I.264, A.308, R.309 Chain B: E.242, R.246 14 PLIP interactions: 14 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:K.64, A:T.65, A:T.65, A:T.65, A:L.66 Salt bridges: A:K.64, A:R.309, A:R.309 AGS.3: 23 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, Q.124, A.189, L.256, I.264, P.268, N.270, A.308, R.309, R.312 Chain C: E.242, R.246 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:I.18, B:Q.20, B:G.61, B:S.62, 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:R.309, C:R.246, C:R.246 Salt bridges: B:K.64, B:R.309, B:R.309 AGS.4: 23 residues within 4Å: Chain C: 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, L.256, I.264, P.268, A.308, R.309, R.312 Chain D: E.48, E.155, E.242, R.246 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:I.18, C:G.61, C:S.62, C:S.62, C:G.63, C:K.64, C:K.64, C:T.65, C:T.65, C:L.66, C:R.309, D:E.48, D:R.246, D:R.246 Salt bridges: C:K.64, C:R.309, C:R.309 AGS.5: 23 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, Q.124, A.189, I.264, P.268, N.270, A.308, R.309, R.312 Chain E: E.155, E.242, R.246 17 PLIP interactions: 15 interactions with chain D, 2 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:L.66, D:Q.124, D:R.309, E:R.246, E:R.246 Salt bridges: D:K.64, D:R.309, D:R.309 AGS.6: 18 residues within 4Å: Chain E: V.17, I.18, Q.20, P.59, T.60, G.61, S.62, G.63, K.64, T.65, L.66, Q.124, L.256, I.264, A.308, R.309 Chain F: L.151, R.246 16 PLIP interactions: 15 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:I.18, E:G.61, E:S.62, E:S.62, E:G.63, E:K.64, E:T.65, E:T.65, E:T.65, E:L.66, E:Q.124, E:R.309, F:R.246 Salt bridges: E:K.64, E:R.309, E:R.309

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

ADP.7: 18 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, Y.121, D.123, I.264, P.268, A.308, R.309, R.312 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:I.18, F:I.18, F:G.61, F:S.62, F:G.63, F:K.64, F:T.65, F:T.65, F:T.65, F:L.66, F:Y.121, F:Y.121 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

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

ATP-dependent Clp protease ATP-binding subunit ClpX

ATP-dependent Clp protease proteolytic subunit

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