SMTL ID : 5kpz.1

PANK3-ADP-PhosphoPantothenate complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x PAZ: N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanine(Non-covalent)

PAZ.1: 16 residues within 4Å: Chain A: G.28, E.146, S.200, G.201, V.202, S.203, R.215, G.218, T.219, S.220 Chain B: I.261, L.271, V.276, A.277 Ligands: ADP.2, MG.3 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.28, A:S.200, A:G.201, A:V.202, A:R.215, B:A.277 Water bridges: A:E.146, A:N.197, A:G.199, A:G.199, A:R.215, A:S.220 Salt bridges: A:R.215 Hydrophobic interactions: B:L.271, B:A.277 PAZ.4: 16 residues within 4Å: Chain A: I.261, L.271, V.276, A.277 Chain B: G.28, E.146, S.200, G.201, V.202, S.203, R.215, G.218, T.219, S.220 Ligands: ADP.5, MG.6 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.28, B:S.200, B:G.201, B:V.202, B:R.215, A:A.277 Water bridges: B:N.197, B:G.199, B:G.199, B:R.215, B:S.220 Salt bridges: B:R.215 Hydrophobic interactions: A:L.271, A:A.277

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

ADP.2: 18 residues within 4Å: Chain A: G.27, G.28, T.29, L.30, K.32, R.94, G.199, S.200, G.223, G.224, F.239, E.240, G.329, N.330, F.331, R.333 Ligands: PAZ.1, MG.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.28, A:T.29, A:L.30, A:L.30, A:R.94, A:G.199, A:S.200, A:G.223, A:E.240, A:N.330, A:N.330, A:F.331, A:R.333 Water bridges: A:K.32 Salt bridges: A:K.32, A:K.32 pi-Stacking: A:F.239 ADP.5: 18 residues within 4Å: Chain B: G.27, G.28, T.29, L.30, K.32, R.94, G.199, S.200, G.223, G.224, F.239, E.240, G.329, N.330, F.331, R.333 Ligands: PAZ.4, MG.6 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:G.28, B:T.29, B:L.30, B:L.30, B:R.94, B:G.199, B:S.200, B:G.223, B:E.240, B:N.330, B:N.330, B:F.331, B:R.333 Water bridges: B:K.32 Salt bridges: B:K.32, B:K.32 pi-Stacking: B:F.239

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.25, E.146 Ligands: PAZ.1, ADP.2 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain B: D.25, E.146 Ligands: PAZ.4, ADP.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Subramanian, C. et al., Allosteric Regulation of Mammalian Pantothenate Kinase. J.Biol.Chem. (2016)

Release Date

2016-08-31

Peptides

Pantothenate kinase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pantothenate kinase 3

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