SMTL ID : 4nb4.2 (3 other biounits)

Pantothenamide-bound Pantothenate kinase from Staphylococcus aureus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: G.26, G.27, T.28, L.29, K.31, L.46, G.116, T.117, G.139, G.140, Q.143, Y.155, G.242, S.243, S.244 Ligands: SH3.2, MG.4 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.27, A:T.28, A:L.29, A:L.29, A:T.117, A:G.139, A:Q.143, A:Y.155, A:S.243, A:S.243, A:S.244 Water bridges: A:K.31, A:K.31, A:K.31, A:N.114, A:S.243 Salt bridges: A:K.31, A:K.31 pi-Stacking: A:Y.155, A:Y.155 ADP.5: 17 residues within 4Å: Chain B: G.26, G.27, T.28, L.29, K.31, L.46, G.116, T.117, G.139, G.140, Q.143, Y.155, G.242, S.243, S.244 Ligands: SH3.3, MG.6 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:G.27, B:T.28, B:T.28, B:T.28, B:L.29, B:L.29, B:T.117, B:T.117, B:G.139, B:Q.143, B:S.243, B:S.243, B:S.244 Water bridges: B:K.31 Salt bridges: B:K.31, B:K.31 pi-Stacking: B:Y.155, B:Y.155

2 x SH3: N-[2-(1,3-benzodioxol-5-yl)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide(Non-covalent)

SH3.2: 22 residues within 4Å: Chain A: G.27, E.88, F.89, G.116, T.117, G.118, T.119, S.120, R.131, G.134, I.135 Chain B: V.174, I.177, I.185, L.189, T.190, A.191, E.220, T.224, Y.258 Ligands: ADP.1, MG.4 24 PLIP interactions: 12 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:F.89, B:V.174, B:I.185, B:A.191, B:E.220, B:E.220 Hydrogen bonds: A:G.27, A:T.117, A:G.118, A:R.131, A:R.131, B:T.190, B:T.190, B:T.190, B:A.191 Water bridges: A:E.88, A:E.88, A:N.114, A:N.114, A:G.116, A:G.116, B:R.167, B:Y.258 pi-Stacking: B:Y.258 SH3.3: 21 residues within 4Å: Chain A: V.174, I.177, L.189, T.190, A.191, E.220, T.224, Y.258 Chain B: G.27, E.88, F.89, G.116, T.117, G.118, T.119, S.120, R.131, G.134, I.135 Ligands: ADP.5, MG.6 19 PLIP interactions: 8 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:V.174, A:E.220, A:E.220, B:F.89, B:I.135 Hydrogen bonds: A:T.190, A:T.190, A:A.191, B:G.27, B:T.117, B:G.118, B:T.119, B:R.131, B:R.131 Water bridges: A:E.220, B:N.114, B:G.116, B:G.116 pi-Stacking: A:Y.258

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

MG.4: 2 residues within 4Å: Ligands: ADP.1, SH3.2 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain B: K.31, E.88 Ligands: SH3.3, ADP.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hughes, S.J. et al., Structural characterization of a new N-substituted pantothenamide bound to pantothenate kinases from Klebsiella pneumoniae and Staphylococcus aureus. Proteins (2014)

Release Date

2014-03-05

Peptides

Type II pantothenate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Type II pantothenate kinase

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