SMTL ID : 9dvy.1

Human mitochondrial ClpX with endogenous substrate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: T.155 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.155 MG.3: 2 residues within 4Å: Chain B: T.155 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.155 MG.5: 2 residues within 4Å: Chain C: T.155 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.155 MG.7: 2 residues within 4Å: Chain D: T.155 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.155

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 21 residues within 4Å: Chain A: Y.34, V.35, V.36, G.37, Q.38, T.150, G.151, S.152, G.153, K.154, T.155, L.156, L.364, I.372, A.416, R.417 Chain B: E.140, E.244, E.350, R.354 Ligands: MG.1 17 PLIP interactions: 2 interactions with chain B, 15 interactions with chain A Hydrogen bonds: B:E.140, A:V.36, A:G.37, A:P.149, A:G.151, A:S.152, A:S.152, A:G.153, A:K.154, A:T.155, A:L.156 Salt bridges: B:R.354, A:K.154, A:K.154, A:R.417, A:R.417, A:R.417 ATP.4: 18 residues within 4Å: Chain B: Y.34, V.35, V.36, P.149, T.150, G.151, S.152, G.153, K.154, T.155, L.156, Q.214, I.372, A.416, R.417 Chain C: E.350, R.354 Ligands: MG.3 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:V.36, B:P.149, B:G.151, B:S.152, B:S.152, B:G.153, B:K.154, B:T.155, B:L.156, B:Q.214 Salt bridges: B:K.154, B:K.154, B:R.417, B:R.417, C:R.354 ATP.6: 19 residues within 4Å: Chain C: Y.34, V.35, V.36, Q.38, P.149, T.150, G.151, S.152, G.153, K.154, T.155, L.156, L.364, I.372, A.416, R.417 Chain D: E.350, R.354 Ligands: MG.5 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:V.36, C:P.149, C:G.151, C:S.152, C:S.152, C:G.153, C:G.153, C:K.154, C:T.155, C:L.156, D:E.350 Salt bridges: C:K.154, C:K.154, C:R.417, C:R.417, C:R.417, D:R.354 ATP.8: 19 residues within 4Å: Chain D: Y.34, V.35, V.36, Q.38, P.149, T.150, G.151, S.152, G.153, K.154, T.155, L.156, I.372, A.416, R.417 Chain E: E.140, E.350, R.354 Ligands: MG.7 18 PLIP interactions: 2 interactions with chain E, 16 interactions with chain D Hydrogen bonds: E:E.140, D:V.36, D:G.37, D:P.149, D:G.151, D:S.152, D:S.152, D:G.153, D:G.153, D:K.154, D:T.155, D:L.156 Salt bridges: E:R.354, D:K.154, D:K.154, D:R.417, D:R.417, D:R.417

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

ADP.9: 14 residues within 4Å: Chain E: Y.34, V.35, V.36, T.150, G.151, S.152, G.153, K.154, T.155, L.156, L.364, I.372, A.416, R.417 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:V.36, E:V.36, E:Q.38, E:G.151, E:G.151, E:S.152, E:G.153, E:K.154, E:T.155, E:L.156 Salt bridges: E:K.154, E:R.417

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, W.C. et al., Assembly and proteolytic activation human ClpXP defined by cryo-EM. To Be Published

Release Date

2025-10-15

Peptides

ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial: ABCDEF
Unidentified endogenous substrate: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial

Unidentified endogenous substrate

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