SMTL ID : 4ne2.2 (1 other biounit)

Pantothenamide-bound Pantothenate Kinase from Klebsiella pneumoniae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: N.61, D.63, L.64, Y.73, S.114, V.115, A.116, V.117, G.118, K.119, S.120, T.121, R.261, K.321, H.325 Ligands: MG.3 30 PLIP interactions: 30 interactions with chain A Hydrogen bonds: A:N.61, A:Y.73, A:Y.73, A:S.114, A:A.116, A:V.117, A:G.118, A:K.119, A:S.120, A:T.121, A:T.121, A:K.321 Water bridges: A:D.63, A:D.63, A:K.119, A:K.119, A:E.217, A:N.260, A:N.260, A:N.260, A:R.261, A:R.261, A:R.261, A:R.261, A:K.264 Salt bridges: A:K.119, A:R.261, A:R.261 pi-Cation interactions: A:H.325, A:H.325 ADP.4: 16 residues within 4Å: Chain B: N.61, D.63, L.64, Y.73, S.114, V.115, A.116, V.117, G.118, K.119, S.120, T.121, R.261, K.321, H.325 Ligands: MG.6 27 PLIP interactions: 27 interactions with chain B Hydrogen bonds: B:N.61, B:Y.73, B:S.114, B:A.116, B:V.117, B:G.118, B:K.119, B:S.120, B:T.121, B:T.121, B:K.321 Water bridges: B:K.119, B:K.119, B:E.217, B:N.260, B:N.260, B:N.260, B:R.261, B:R.261, B:R.261, B:R.261, B:K.264 Salt bridges: B:K.119, B:R.261, B:R.261 pi-Cation interactions: B:H.325, B:H.325

2 x SH2: (R)-N-(3-((2-(benzo[d][1,3]dioxol-5-yl)ethyl)amino)-3-oxopropyl)-2,4-dihydroxy-3,3-dimethylbutanamide(Non-covalent)

SH2.2: 16 residues within 4Å: Chain A: V.115, D.145, L.148, K.163, G.164, Y.169, Y.193, Y.198, L.219, Y.258, R.261, F.262, F.265, F.277, L.295, N.300 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:D.145, A:L.148, A:Y.193, A:Y.198, A:F.262 Hydrogen bonds: A:K.163, A:Y.169, A:Y.169, A:Y.198, A:R.261, A:N.300 Water bridges: A:Y.198, A:L.219, A:L.219, A:N.303 pi-Stacking: A:F.277 SH2.5: 16 residues within 4Å: Chain B: V.115, D.145, L.148, K.163, G.164, Y.169, Y.193, Y.198, L.219, Y.258, R.261, F.262, F.265, F.277, L.295, N.300 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:D.145, B:L.148, B:Y.193, B:Y.198, B:F.262 Hydrogen bonds: B:K.163, B:Y.169, B:Y.198, B:Y.198, B:Y.258, B:R.261, B:N.300 Water bridges: B:L.219, B:L.219, B:N.303 pi-Stacking: B:F.277

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: S.120, E.217 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.120, H2O.4, H2O.4, H2O.4, H2O.4 MG.6: 3 residues within 4Å: Chain B: S.120, E.217 Ligands: ADP.4 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.120, H2O.12, H2O.12, H2O.12, H2O.12

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

2014-02-26

Peptides

Pantothenate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

Pantothenate kinase

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