SMTL ID : 5jic.1

Staphylococcus aureus Type II pantothenate kinase in complex with a pantothenate analog

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.70 Ligands: ADP.2, N7E.3 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: E.70 Ligands: ADP.5, N7E.6 No protein-ligand interaction detected (PLIP)

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

ADP.2: 18 residues within 4Å: Chain A: G.8, G.9, T.10, L.11, K.13, L.28, G.98, T.99, G.121, G.122, Q.125, Y.137, G.224, S.225, S.226, H.228 Ligands: MG.1, N7E.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.9, A:T.10, A:T.10, A:L.11, A:L.11, A:T.99, A:G.121, A:Q.125, A:S.225, A:S.226 Water bridges: A:K.13, A:K.13, A:N.96, A:Y.137, A:S.225 Salt bridges: A:K.13, A:K.13 pi-Stacking: A:Y.137, A:Y.137 ADP.5: 18 residues within 4Å: Chain B: G.8, G.9, T.10, L.11, K.13, L.28, G.98, T.99, G.121, G.122, Q.125, Y.137, G.224, S.225, S.226, H.228 Ligands: MG.4, N7E.6 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:G.9, B:T.10, B:T.10, B:T.10, B:L.11, B:L.11, B:T.99, B:T.99, B:G.121, B:Q.125, B:S.225, B:S.226 Water bridges: B:K.13, B:K.13, B:N.96, B:S.225 Salt bridges: B:K.13, B:K.13 pi-Stacking: B:Y.137, B:Y.137

2 x N7E: N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(5-methoxypentyl)-beta-alaninamide(Non-covalent)

N7E.3: 22 residues within 4Å: Chain A: G.9, E.70, F.71, G.98, T.99, G.100, T.101, S.102, R.113, G.116, I.117 Chain B: V.156, I.159, I.167, D.170, L.171, T.172, A.173, E.202, Y.240 Ligands: MG.1, ADP.2 19 PLIP interactions: 9 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:V.156, B:I.167, B:E.202, B:Y.240, A:F.71 Hydrogen bonds: B:T.172, B:T.172, B:T.172, B:A.173, A:G.9, A:T.99, A:G.100, A:R.113, A:R.113 Water bridges: B:Y.240, A:K.13, A:E.70, A:N.96, A:G.98 N7E.6: 22 residues within 4Å: Chain A: V.156, I.159, I.167, D.170, L.171, T.172, A.173, E.202, Y.240 Chain B: G.9, E.70, F.71, G.98, T.99, G.100, T.101, S.102, R.113, G.116, I.117 Ligands: MG.4, ADP.5 16 PLIP interactions: 7 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:V.156, A:I.167, A:E.202, A:Y.240, B:F.71 Hydrogen bonds: A:T.172, A:T.172, A:A.173, B:G.9, B:T.99, B:G.100, B:R.113, B:R.113 Water bridges: B:K.13, B:N.96, B:G.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hughes, S.J. et al., Discovery of Potent Pantothenamide Inhibitors of Staphylococcus aureus Pantothenate Kinase through a Minimal SAR Study: Inhibition Is Due to Trapping of the Product. Acs Infect Dis. (2016)

Release Date

2016-08-10

Peptides

Type II pantothenate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Type II pantothenate kinase

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