SMTL ID : 7mp9.1

Crystal structure of the cytosolic domain of Tribolium castaneum PINK1 phosphorylated at Ser205 in complex with ADP analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: K.224, N.227, D.244 Chain B: S.90 Ligands: AN2.9 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.90 MG.10: 5 residues within 4Å: Chain A: S.90 Chain B: K.224, N.227, D.244 Ligands: AN2.18 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.90

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: N.407, K.408, N.417, W.418, R.419 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.408, A:N.417, A:N.417 Salt bridges: A:R.419 SO4.3: 2 residues within 4Å: Chain A: K.51, R.181 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.51, A:R.181 SO4.4: 5 residues within 4Å: Chain A: S.23, P.130, H.212, H.216, C.433 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.212, A:H.216 SO4.5: 2 residues within 4Å: Chain A: R.441, H.445 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.441, A:H.445 SO4.11: 5 residues within 4Å: Chain B: N.407, K.408, N.417, W.418, R.419 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.408, B:N.417, B:N.417 Salt bridges: B:R.419 SO4.12: 2 residues within 4Å: Chain B: K.51, R.181 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.51, B:R.181 SO4.13: 5 residues within 4Å: Chain B: S.23, P.130, H.212, H.216, C.433 3 PLIP interactions: 3 interactions with chain B Water bridges: B:H.212 Salt bridges: B:H.212, B:H.216 SO4.14: 2 residues within 4Å: Chain B: R.441, H.445 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.441, B:H.445

6 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 11 residues within 4Å: Chain A: Y.30, D.33, F.37, R.107, H.132, P.133, I.135, A.137, F.139, K.180, Y.182 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.30, A:R.107, A:R.107, A:I.135 Water bridges: A:H.132 PG4.7: 8 residues within 4Å: Chain A: K.51, I.53, R.181, Y.182, D.183, C.184, N.185 Ligands: AN2.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.51, A:R.181, A:N.185 PG4.8: 6 residues within 4Å: Chain A: R.197, W.370, L.395, T.421, E.424, Y.425 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.197, A:R.197 PG4.15: 11 residues within 4Å: Chain B: Y.30, D.33, F.37, R.107, H.132, P.133, I.135, A.137, F.139, K.180, Y.182 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.107, B:R.107, B:I.135 Water bridges: B:H.132 PG4.16: 8 residues within 4Å: Chain B: K.51, I.53, R.181, Y.182, D.183, C.184, N.185 Ligands: AN2.18 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.51, B:R.181, B:N.185 PG4.17: 6 residues within 4Å: Chain B: R.197, W.370, L.395, T.421, E.424, Y.425 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.197, B:R.197

2 x AN2: AMP PHOSPHORAMIDATE(Non-covalent)

AN2.9: 20 residues within 4Å: Chain A: I.53, A.54, N.58, G.59, V.61, A.79, K.81, M.179, K.180, R.181, Y.182, N.185, D.226, N.227, L.229, S.243, D.244 Chain B: S.90 Ligands: MG.1, PG4.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.59, A:G.59, A:K.180, A:Y.182, A:N.185, A:D.226 Water bridges: A:K.81 Salt bridges: A:K.81 AN2.18: 20 residues within 4Å: Chain A: S.90 Chain B: I.53, A.54, N.58, G.59, V.61, A.79, K.81, M.179, K.180, R.181, Y.182, N.185, D.226, N.227, L.229, S.243, D.244 Ligands: MG.10, PG4.16 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.59, B:G.59, B:K.180, B:Y.182, B:N.185, B:D.226 Water bridges: B:K.81 Salt bridges: B:K.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rasool, S. et al., Mechanism of PINK1 activation by autophosphorylation and insights into assembly on the TOM complex. Mol.Cell (2022)

Release Date

2021-12-01

Peptides

Serine/threonine-protein kinase PINK1, mitochondrial-like Protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Serine/threonine-protein kinase PINK1, mitochondrial-like Protein

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