SMTL ID : 6pp6.1

ClpX in ClpX-ClpP complex bound to substrate and ATP-gamma-S, class 3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

UNK-UNK-HIS-UNK-UNK-UNK-UNK.1: 17 residues within 4Å: Chain A: N.134, P.135, R.139 Chain B: Y.92, V.93, T.138, V.141 Chain C: G.91, Y.92, V.93, V.141 Chain D: G.91, Y.92, V.93 Chain E: G.91, Y.92, V.93 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: E:Y.92, A:N.134, B:V.93

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

AGS.2: 21 residues within 4Å: Chain A: V.17, I.18, T.60, G.61, S.62, G.63, K.64, T.65, L.66, Y.121, D.123, Q.124, A.189, L.256, I.264, N.270, A.308, R.309, R.312 Chain B: E.242, R.246 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.61, A:S.62, A:S.62, A:G.63, A:K.64, A:K.64, A:T.65, A:T.65, A:L.66, A:D.123, A:R.309, B:E.242 Salt bridges: A:K.64, A:R.309, A:R.309 AGS.3: 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, Q.124, A.189, L.256, I.264, P.268, L.272, A.308, R.309 Chain C: E.242, R.246 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:I.18, B:G.61, B:S.62, B:S.62, B:G.63, B:K.64, B:T.65, B:T.65, B:T.65, B:L.66, B:R.309, B:R.309, C:R.246 Salt bridges: B:K.64, B:R.309, B:R.309 AGS.4: 21 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 Chain D: E.48, E.242, R.246 19 PLIP interactions: 17 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:I.18, 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:T.65, C:L.66, C:D.123, C:R.309, D:E.48, D:R.246 Salt bridges: C:K.64, C:R.309, C:R.309 AGS.5: 22 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, D.123, Q.124, A.189, I.264, P.268, A.308, R.309, R.312 Chain E: E.242, R.246 20 PLIP interactions: 18 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:I.18, D:G.61, D:S.62, 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:D.123, 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: Y.16, V.17, I.18, Q.20, T.60, G.61, S.62, G.63, K.64, T.65, L.66, Y.121, Q.124, L.256, I.264, A.308, R.309 Chain F: R.246 17 PLIP interactions: 15 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:I.18, E:Q.20, E:G.61, E:S.62, E:S.62, E:G.63, E:K.64, E:T.65, E:T.65, E:L.66, E:R.309, E:R.309, F:R.246 Salt bridges: E:K.64, E:R.309, E:R.309, F:R.246

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

ADP.7: 15 residues within 4Å: Chain F: Y.16, V.17, I.18, T.60, G.61, S.62, G.63, K.64, T.65, L.66, I.264, P.268, A.308, R.309, R.312 10 PLIP interactions: 10 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 Salt bridges: F:K.64

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

ATP-dependent Clp protease ATP-binding subunit ClpX

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