SMTL ID : 4gi7.1 (3 other biounits)

Crystal structure of Klebsiella pneumoniae pantothenate kinase in complex with a pantothenate analogue

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 17 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: UNX.4, UNX.5 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.61, A:Y.73, A:Y.73, A:A.116, A:V.117, A:G.118, A:K.119, A:S.120, A:T.121, A:T.121, A:K.321 Salt bridges: A:K.119, A:R.261, A:R.261 pi-Stacking: A:H.325, A:H.325 ADP.7: 15 residues within 4Å: Chain B: N.61, D.63, Y.73, S.114, A.116, V.117, G.118, K.119, S.120, T.121, R.261, K.321, H.325 Ligands: UNX.11, UNX.12 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:N.61, 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, B:K.321 Water bridges: B:Y.73 Salt bridges: B:K.119, B:R.261, B:R.261 pi-Stacking: B:H.325, B:H.325

2 x 0JR: (2R)-2,4-dihydroxy-3,3-dimethyl-N-{3-oxo-3-[(pyridin-3-ylmethyl)amino]propyl}butanamide(Non-covalent)

0JR.2: 17 residues within 4Å: Chain A: D.145, L.148, K.163, G.164, H.195, Y.198, L.219, Y.258, Y.276, F.277, Y.280, L.295, I.299, N.300 Ligands: UNX.4, UNX.5, UNX.6 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.148, A:L.219, A:Y.276, A:F.277, A:Y.280, A:I.299 Hydrogen bonds: A:Y.198, A:Y.198, A:N.300, A:N.300 Water bridges: A:D.145, A:Y.193 pi-Stacking: A:Y.198 0JR.8: 16 residues within 4Å: Chain B: V.115, D.145, K.163, G.164, H.195, Y.198, L.219, Y.258, R.261, F.262, F.265, F.277, I.299, N.300 Ligands: UNX.11, UNX.12 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.198, B:I.299 Hydrogen bonds: B:H.195, B:Y.198, B:Y.258, B:N.300, B:N.300 Water bridges: B:D.145, B:R.261 pi-Stacking: B:F.277

11 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.3: 4 residues within 4Å: Chain A: T.144, D.145, Y.169 Ligands: UNX.6 No protein-ligand interaction detected (PLIP) UNX.4: 6 residues within 4Å: Chain A: V.115, K.119 Ligands: ADP.1, 0JR.2, UNX.5, UNX.6 No protein-ligand interaction detected (PLIP) UNX.5: 5 residues within 4Å: Chain A: H.195, R.261 Ligands: ADP.1, 0JR.2, UNX.4 No protein-ligand interaction detected (PLIP) UNX.6: 6 residues within 4Å: Chain A: K.119, D.145, E.217 Ligands: 0JR.2, UNX.3, UNX.4 No protein-ligand interaction detected (PLIP) UNX.9: 6 residues within 4Å: Chain B: T.143, T.144, D.145, E.217, G.218 Ligands: UNX.13 No protein-ligand interaction detected (PLIP) UNX.10: 1 residues within 4Å: Chain B: W.38 No protein-ligand interaction detected (PLIP) UNX.11: 6 residues within 4Å: Chain B: V.115, H.195, R.261 Ligands: ADP.7, 0JR.8, UNX.12 No protein-ligand interaction detected (PLIP) UNX.12: 5 residues within 4Å: Chain B: V.115, K.119 Ligands: ADP.7, 0JR.8, UNX.11 No protein-ligand interaction detected (PLIP) UNX.13: 4 residues within 4Å: Chain B: T.144, D.145, Y.169 Ligands: UNX.9 No protein-ligand interaction detected (PLIP) UNX.14: 2 residues within 4Å: Chain A: K.334 Chain B: L.94 No protein-ligand interaction detected (PLIP) UNX.15: 3 residues within 4Å: Chain B: R.314, S.316, R.333 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, B. et al., Crystal structures of Klebsiella pneumoniae pantothenate kinase in complex with N-substituted pantothenamides. Proteins (2013)

Release Date

2013-04-10

Peptides

Pantothenate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Pantothenate kinase

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