SMTL ID : 7p0m.1

Human mitochondrial Lon protease with substrate in the ATPase and protease domains

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-7-mer

Ligands

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

ATP.1: 22 residues within 4Å: Chain A: H.427, Y.428, M.430, P.460, P.461, G.462, V.463, G.464, K.465, T.466, S.467, E.527, N.576, Y.597, I.605, Y.609, V.645, R.646, Q.649 Chain B: E.550, R.588 Ligands: MG.2 22 PLIP interactions: 19 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Y.428, A:G.462, A:V.463, A:G.464, A:G.464, A:K.465, A:T.466, A:S.467, A:S.467, A:S.467, A:N.576, A:Y.597, A:Y.597, B:E.550, B:E.550 Salt bridges: A:K.465, A:K.465, A:R.646, A:R.646, A:R.646, B:R.588 pi-Cation interactions: A:H.427 ATP.3: 20 residues within 4Å: Chain B: D.426, H.427, Y.428, P.461, G.462, V.463, G.464, K.465, T.466, S.467, N.576, Y.597, I.605, Y.609, V.645, R.646, Q.649 Chain C: E.550, R.588 Ligands: MG.4 17 PLIP interactions: 2 interactions with chain C, 15 interactions with chain B Hydrogen bonds: C:E.550, B:Y.428, B:G.462, B:V.463, B:G.464, B:K.465, B:T.466, B:S.467, B:Y.597, B:Q.649 Salt bridges: C:R.588, B:K.465, B:K.465, B:R.646, B:R.646, B:R.646 pi-Cation interactions: B:H.427 ATP.5: 22 residues within 4Å: Chain C: D.426, H.427, Y.428, P.460, P.461, G.462, V.463, G.464, K.465, T.466, S.467, E.527, N.576, Y.597, I.605, Y.609, V.645, R.646, Q.649 Chain D: E.550, R.588 Ligands: MG.6 21 PLIP interactions: 19 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Y.428, C:G.462, C:V.463, C:G.464, C:K.465, C:T.466, C:S.467, C:S.467, C:N.576, C:Y.597, C:Y.597, C:Q.649, D:E.550 Salt bridges: C:K.465, C:K.465, C:R.646, C:R.646, C:R.646, D:R.588 pi-Cation interactions: C:H.427, C:H.427 ATP.9: 19 residues within 4Å: Chain F: H.427, Y.428, M.430, P.461, G.462, V.463, G.464, K.465, T.466, S.467, N.576, Y.597, I.605, Y.609, Q.613, V.645, R.646, Q.649 Ligands: MG.10 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:Y.428, F:G.462, F:V.463, F:G.464, F:K.465, F:T.466, F:S.467, F:Y.597, F:Y.597, F:Q.649 Salt bridges: F:K.465, F:K.465, F:R.646, F:R.646, F:R.646 pi-Stacking: F:H.427, F:Y.609

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.466, D.526, E.527 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.466 MG.4: 3 residues within 4Å: Chain B: T.466, T.574 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.466 MG.6: 4 residues within 4Å: Chain C: T.466, E.527, T.574 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.466 MG.10: 3 residues within 4Å: Chain F: T.466, D.526 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.466

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

ADP.7: 15 residues within 4Å: Chain D: D.426, H.427, Y.428, P.461, G.462, V.463, G.464, K.465, T.466, S.467, Y.597, I.605, Y.609, V.645, R.646 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:Y.428, D:G.462, D:V.463, D:G.464, D:K.465, D:T.466, D:T.466, D:S.467, D:Y.597, D:Y.597 Salt bridges: D:K.465, D:R.646, D:R.646 pi-Cation interactions: D:H.427 ADP.8: 16 residues within 4Å: Chain E: H.427, Y.428, P.461, G.462, V.463, G.464, K.465, T.466, S.467, Y.597, I.605, Y.609, L.610, Q.613, V.645, R.646 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:Y.428, E:G.462, E:V.463, E:G.464, E:K.465, E:T.466, E:S.467, E:S.467, E:Y.597, E:Y.597 Salt bridges: E:K.465, E:R.646, E:R.646 pi-Stacking: E:H.427

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Valentin Gese, G. et al., A dual allosteric pathway drives human mitochondrial Lon. To Be Published

Release Date

2021-08-11

Peptides

Lon protease homolog, mitochondrial: ABCDEF
Unknown peptide from human mitochondrial transcription factor A (TFAM): GHIJKLM

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
I

I
J

J
M

K
H

L
L

M
K

Lon protease homolog, mitochondrial

Unknown peptide from human mitochondrial transcription factor A (TFAM)

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