SMTL ID : 7ue8.1

PANK3 complex structure with compound PZ-3890

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 21 residues within 4Å: Chain A: G.27, G.28, T.29, L.30, K.32, E.146, I.198, G.199, S.200, G.201, G.223, G.224, L.227, F.239, G.329, N.330, F.331, R.333 Chain B: I.261 Ligands: MG.2, EDO.5 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.28, A:T.29, A:T.29, A:L.30, A:L.30, A:K.32, A:S.200, A:S.200, A:G.201, A:G.223, A:E.240, A:N.330, A:N.330, A:F.331, A:R.333 Water bridges: A:K.32, A:E.146, A:N.197, A:N.197, A:G.199, A:S.200, A:R.333 Salt bridges: A:K.32 pi-Stacking: A:F.239 ANP.6: 21 residues within 4Å: Chain A: I.261 Chain B: G.27, G.28, T.29, L.30, K.32, E.146, I.198, G.199, S.200, G.201, G.223, G.224, L.227, F.239, G.329, N.330, F.331, R.333 Ligands: MG.7, EDO.10 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:G.28, B:T.29, B:L.30, B:L.30, B:K.32, B:S.200, B:S.200, B:G.201, B:G.223, B:E.240, B:N.330, B:N.330, B:F.331, B:R.333 Water bridges: B:K.32, B:N.197, B:N.197, B:G.199, B:S.200, B:R.333 Salt bridges: B:K.32 pi-Stacking: B:F.239

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: K.32 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: K.32 Ligands: ANP.6 No protein-ligand interaction detected (PLIP)

2 x Y92: 1-[4-(6-chloropyridazin-3-yl)piperazin-1-yl]-2-(4-cyclopropyl-3-fluorophenyl)ethan-1-one(Non-covalent)

Y92.3: 19 residues within 4Å: Chain A: E.146, G.201, V.202, S.203, R.215, T.217, G.218, T.219 Chain B: Y.262, L.271, V.276, A.277, N.307, G.310, S.311, R.314, A.345, L.346, W.349 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.262, B:L.271, B:A.277, B:A.345 Hydrogen bonds: B:R.314, A:R.215, A:R.215 pi-Stacking: B:W.349 pi-Cation interactions: A:R.215 Y92.8: 19 residues within 4Å: Chain A: Y.262, L.271, V.276, A.277, N.307, G.310, S.311, R.314, A.345, L.346, W.349 Chain B: E.146, G.201, V.202, S.203, R.215, T.217, G.218, T.219 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.262, A:L.271, A:A.277, A:A.345 Hydrogen bonds: A:R.314, B:R.215, B:R.215 pi-Stacking: A:W.349 pi-Cation interactions: B:R.215

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 9 residues within 4Å: Chain A: D.25, L.150, N.197, G.329, E.362, G.363, Y.364, F.365, G.366 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.25, A:E.362, A:F.365, A:G.366 Water bridges: A:A.367 ACT.9: 9 residues within 4Å: Chain B: D.25, L.150, N.197, G.329, E.362, G.363, Y.364, F.365, G.366 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.362, B:F.365, B:G.366 Water bridges: B:A.367

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 6 residues within 4Å: Chain A: L.30, T.69, R.94, F.95, P.96 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.94 EDO.10: 6 residues within 4Å: Chain B: L.30, T.69, R.94, F.95, P.96 Ligands: ANP.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Subramanian, C. et al., Relief of CoA sequestration and restoration of mitochondrial function in a mouse model of propionic acidemia. J Inherit Metab Dis (2023)

Release Date

2023-03-29

Peptides

Pantothenate kinase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pantothenate kinase 3

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