SMTL ID : 6avp.1 (1 other biounit)

Staphylococcus aureus Type II pantothenate kinase in complex with ADP and pantothenate analog Phosphate-MeO-N5Pan

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: G.8, G.9, T.10, L.11, K.13, V.97, G.98, T.99, G.121, G.122, Q.125, Y.137, G.224, S.225, S.226 Ligands: N7E.2, MG.3 15 PLIP interactions: 15 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 Salt bridges: A:K.13, A:K.13 pi-Stacking: A:Y.137, A:Y.137 ADP.4: 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: N7E.5, MG.6 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:G.9, 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.225, B:S.226, B:H.228 Water bridges: B:K.13, B:K.13 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.2: 20 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, L.171, T.172, A.173, E.202, Y.240 Ligands: ADP.1, MG.3 19 PLIP interactions: 9 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:V.156, B:L.171, B:Y.240, A:F.71 Hydrogen bonds: B:T.172, B:T.172, B:T.172, B:A.173, A:G.9, A:G.100, A:T.101, A:R.113, A:R.113 Water bridges: B:Y.160, B:Y.160, A:E.70, A:E.70, A:N.96, A:G.98 N7E.5: 21 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, T.99, G.100, T.101, S.102, R.113, G.116, I.117 Ligands: ADP.4, MG.6 18 PLIP interactions: 9 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:F.71, A:V.156, A:I.167, A:L.171, A:E.202, A:Y.240 Hydrogen bonds: B:G.9, B:T.99, B:G.100, B:T.101, B:R.113, B:R.113, A:T.172, A:T.172, A:T.172, A:A.173 Water bridges: B:K.13, B:N.96

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.6, K.13 Ligands: ADP.1, N7E.2 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: E.70 Ligands: ADP.4, N7E.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y. et al., Structure-based identification of uncompetitive inhibitors for Staphylococcus aureus pantothenate kinase. To Be Published

Release Date

2018-09-12

Peptides

Type II pantothenate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Type II pantothenate kinase

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