SMTL ID : 6b3v.1

PANK3 complex with compound PZ-2891

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 23 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, E.240, G.329, N.330, F.331, R.333 Chain B: I.261 Ligands: MG.2, EDO.3, 7DQ.5 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:G.28, A:T.29, A:L.30, A:K.32, A:R.94, 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:E.146, A:E.146, A:N.197, A:N.197, A:G.199, A:G.363 Salt bridges: A:K.32 pi-Stacking: A:F.239 ANP.6: 23 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, E.240, G.329, N.330, F.331, R.333 Ligands: MG.7, EDO.8, 7DQ.10 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:G.28, B:T.29, B:L.30, B:K.32, B:R.94, 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:T.29, B:E.146, B:E.146, B:N.197, B:N.197, B:G.199, B:G.363 Salt bridges: B:K.32 pi-Stacking: B:F.239

2 x MG: MAGNESIUM ION(Non-functional Binders)

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

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

EDO.3: 7 residues within 4Å: Chain A: L.30, T.69, I.71, R.94, F.95, P.96 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.94 EDO.4: 5 residues within 4Å: Chain A: D.265, Y.266, E.267, R.268 Chain B: Y.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.265, A:E.267, A:R.268 EDO.8: 7 residues within 4Å: Chain B: L.30, T.69, I.71, R.94, F.95, P.96 Ligands: ANP.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.94 EDO.9: 5 residues within 4Å: Chain A: Y.127 Chain B: D.265, Y.266, E.267, R.268 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.265, B:E.267, B:R.268

2 x 7DQ: 6-(4-{[4-(propan-2-yl)phenyl]acetyl}piperazin-1-yl)pyridazine-3-carbonitrile(Non-covalent)

7DQ.5: 21 residues within 4Å: Chain A: E.146, G.201, V.202, S.203, R.215, G.218, T.219 Chain B: V.258, I.261, Y.266, L.271, V.276, A.277, N.307, G.310, S.311, R.314, A.345, L.346, W.349 Ligands: ANP.1 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.258, B:I.261, B:Y.266, B:L.271, 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 7DQ.10: 21 residues within 4Å: Chain A: V.258, I.261, Y.266, 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, G.218, T.219 Ligands: ANP.6 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:V.258, A:I.261, A:Y.266, A:L.271, 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, L.K. et al., A therapeutic approach to pantothenate kinase associated neurodegeneration. Nat Commun (2018)

Release Date

2018-08-29

Peptides

Pantothenate kinase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pantothenate kinase 3

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