SMTL ID : 7edz.1 (2 other biounits)

Crystal Structure of human PPCS in complex with P-HoPan and AMPPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 20 residues within 4Å: Chain A: L.156, L.177, A.179, V.181, D.183, V.210, P.211, K.212, L.213, L.214, S.229, F.230, K.231, L.232, E.233 Chain B: K.195, Q.197, S.198 Ligands: MG.3, J1O.5 20 PLIP interactions: 6 interactions with chain B, 14 interactions with chain A Hydrogen bonds: B:K.195, B:S.198, B:S.198, A:A.179, A:P.211, A:L.213, A:F.230, A:F.230, A:K.231, A:L.232, A:L.232 Water bridges: B:I.196, B:S.199, A:V.181, A:V.181, A:K.212, A:L.214, A:L.214 Salt bridges: B:K.195, A:K.231 ANP.7: 20 residues within 4Å: Chain A: K.195, Q.197, S.198 Chain B: L.156, L.177, A.179, V.181, D.183, V.210, P.211, K.212, L.213, L.214, S.229, F.230, K.231, L.232, E.233 Ligands: MG.9, J1O.11 20 PLIP interactions: 14 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:A.179, B:P.211, B:L.213, B:F.230, B:F.230, B:K.231, B:L.232, B:L.232, A:K.195, A:S.198, A:S.198 Water bridges: B:V.181, B:V.181, B:K.212, B:L.214, B:L.214, A:I.196, A:S.199 Salt bridges: B:K.231, A:K.195

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

SO4.2: 3 residues within 4Å: Chain A: T.271, S.274, R.302 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.274, A:S.274 Water bridges: A:T.271, A:D.273 Salt bridges: A:R.302 SO4.4: 4 residues within 4Å: Chain A: G.15, A.16, A.17, R.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.15, A:A.17, A:R.18 Salt bridges: A:R.18 SO4.6: 5 residues within 4Å: Chain A: K.46, R.85, R.87, T.150 Chain B: F.60 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.85, A:R.85, A:R.85 Salt bridges: A:K.46, A:R.85, A:R.87 SO4.8: 3 residues within 4Å: Chain B: T.271, S.274, R.302 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.271, B:S.274, B:S.274 Water bridges: B:D.273 Salt bridges: B:R.302 SO4.10: 4 residues within 4Å: Chain B: G.15, A.16, A.17, R.18 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.15, B:A.17, B:R.18 Salt bridges: B:R.18 SO4.12: 5 residues within 4Å: Chain A: F.60 Chain B: K.46, R.85, R.87, T.150 6 PLIP interactions: 6 interactions with chain B Water bridges: B:R.85, B:R.85, B:R.85 Salt bridges: B:K.46, B:R.85, B:R.87

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.183, K.212 Chain B: K.195 Ligands: ANP.1, J1O.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.183, H2O.1, H2O.1 MG.9: 5 residues within 4Å: Chain A: K.195 Chain B: D.183, K.212 Ligands: ANP.7, J1O.11 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.183, H2O.5, H2O.5

2 x J1O: 4-[[(2R)-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]butanoic acid(Non-covalent)

J1O.5: 16 residues within 4Å: Chain A: N.59, S.61, S.62, G.63, R.64, R.65, A.178, A.179, A.180, V.181, F.230, L.232, N.258, R.263 Ligands: ANP.1, MG.3 21 PLIP interactions: 3 interactions with chain B, 18 interactions with chain A Water bridges: B:K.195, B:K.195, A:G.43, A:G.66 Salt bridges: B:K.195, A:R.263 Hydrophobic interactions: A:L.232, A:L.232 Hydrogen bonds: A:N.59, A:S.62, A:S.62, A:S.62, A:G.63, A:R.64, A:R.65, A:R.65, A:R.65, A:A.178, A:A.179, A:V.181, A:N.258 J1O.11: 16 residues within 4Å: Chain B: N.59, S.61, S.62, G.63, R.64, R.65, A.178, A.179, A.180, V.181, F.230, L.232, N.258, R.263 Ligands: ANP.7, MG.9 21 PLIP interactions: 18 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.232, B:L.232 Hydrogen bonds: B:N.59, B:S.62, B:S.62, B:S.62, B:G.63, B:R.64, B:R.65, B:R.65, B:R.65, B:A.178, B:A.179, B:V.181, B:N.258 Water bridges: B:G.43, B:G.66, A:K.195, A:K.195 Salt bridges: B:R.263, A:K.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mostert, K.J. et al., The Coenzyme A Level Modulator Hopantenate (HoPan) Inhibits Phosphopantotenoylcysteine Synthetase Activity. Acs Chem.Biol. (2021)

Release Date

2021-11-24

Peptides

Phosphopantothenate--cysteine ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
D

Phosphopantothenate--cysteine ligase

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