SMTL ID : 4m7y.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

2GH.1: 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, I.167, T.172, A.173, E.202, T.206, Y.240 Ligands: ADP.2 19 PLIP interactions: 12 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:F.71, B:V.156, B:I.167, B:E.202, B:Y.240 Hydrogen bonds: A:G.9, A:T.99, A:G.100, A:T.101, A:R.113, A:R.113, B:T.172, B:A.173 Water bridges: A:E.70, A:N.96, A:G.98, A:G.98, A:S.102, B:Y.240 2GH.15: 18 residues within 4Å: Chain A: V.156, I.167, 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: ADP.16 17 PLIP interactions: 10 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.71, A:V.156, A:E.202, A:Y.240, 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:A.173 Water bridges: B:N.96, B:G.98, B:G.98, A:Y.240

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

ADP.2: 16 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 Ligands: 2GH.1 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.9, A:T.10, A:T.10, A:T.10, A:L.11, A:L.11, A:T.99, A:G.121, A:S.225, A:S.226 Water bridges: A:D.6, A:D.6, A:K.13, A:Q.125, A:Y.137, A:S.225 Salt bridges: A:K.13, A:K.13 pi-Stacking: A:Y.137, A:Y.137 ADP.16: 17 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: 2GH.15 19 PLIP interactions: 19 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:G.121, B:S.225, B:S.225 Water bridges: B:D.6, B:D.6, 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

7 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 8 residues within 4Å: Chain A: R.113, V.114, G.115, G.116 Chain B: R.213, R.244 Ligands: PO4.18, PO4.19 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.115 Water bridges: A:R.113, B:R.213, B:R.244, B:R.244 Salt bridges: A:R.113, B:R.213, B:R.244 PO4.4: 5 residues within 4Å: Chain A: D.88, L.89, A.90, D.91, N.219 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.90, A:D.91, A:N.219 PO4.17: 5 residues within 4Å: Chain B: H.228, N.229, R.234 Ligands: UNX.23, PO4.25 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.229 Salt bridges: B:H.228, B:R.234 PO4.18: 5 residues within 4Å: Chain A: R.112 Chain B: R.213, R.244 Ligands: PO4.3, UNX.20 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.213, B:R.244 PO4.19: 7 residues within 4Å: Chain B: I.167, P.168, L.171, R.244 Ligands: PO4.3, UNX.20, UNX.27 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.244, A:R.113 Water bridges: B:R.244 PO4.25: 3 residues within 4Å: Chain B: H.228, N.229 Ligands: PO4.17 No protein-ligand interaction detected (PLIP) PO4.26: 3 residues within 4Å: Chain B: T.26, H.228, F.256 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.26, B:T.26, B:T.26 Salt bridges: B:H.228

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

UNX.5: 3 residues within 4Å: Chain A: Q.111, R.112, R.113 Ligand excluded by PLIP UNX.6: 2 residues within 4Å: Chain A: Y.249, Y.250 Ligand excluded by PLIP UNX.7: 1 residues within 4Å: Chain A: H.158 Ligand excluded by PLIP UNX.8: 2 residues within 4Å: Chain A: R.213, R.244 Ligand excluded by PLIP UNX.9: 3 residues within 4Å: Chain A: I.14, V.35, W.38 Ligand excluded by PLIP UNX.10: 4 residues within 4Å: Chain A: I.134, T.135, D.136, Q.139 Ligand excluded by PLIP UNX.11: 2 residues within 4Å: Chain A: F.227, R.234 Ligand excluded by PLIP UNX.12: 3 residues within 4Å: Chain A: V.242, G.245, C.246 Ligand excluded by PLIP UNX.13: 2 residues within 4Å: Chain A: Q.66, I.67 Ligand excluded by PLIP UNX.14: 3 residues within 4Å: Chain A: H.158, I.159 Chain B: N.53 Ligand excluded by PLIP UNX.20: 3 residues within 4Å: Chain B: R.244 Ligands: PO4.18, PO4.19 Ligand excluded by PLIP UNX.21: 2 residues within 4Å: Chain B: R.234, E.238 Ligand excluded by PLIP UNX.22: 2 residues within 4Å: Chain B: Y.250 Ligands: UNX.24 Ligand excluded by PLIP UNX.23: 2 residues within 4Å: Chain B: N.253 Ligands: PO4.17 Ligand excluded by PLIP UNX.24: 2 residues within 4Å: Chain B: E.252 Ligands: UNX.22 Ligand excluded by PLIP UNX.27: 2 residues within 4Å: Chain B: L.243 Ligands: PO4.19 Ligand excluded by PLIP UNX.28: 1 residues within 4Å: Chain B: H.146 Ligand excluded by PLIP UNX.29: 1 residues within 4Å: Chain B: W.38 Ligand excluded by PLIP UNX.30: 2 residues within 4Å: Chain B: R.112, R.113 Ligand excluded by PLIP UNX.31: 5 residues within 4Å: Chain A: R.213, R.244 Chain B: R.113, V.114, G.115 Ligand excluded by PLIP UNX.32: 1 residues within 4Å: Chain B: N.219 Ligand excluded by PLIP UNX.33: 3 residues within 4Å: Chain B: Q.66, I.67, F.68 Ligand excluded by PLIP

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

2014-09-03

Peptides

Type II pantothenate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Type II pantothenate kinase

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