SMTL ID : 4nau.1

S. aureus CoaD with Inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-hexamer

Ligands

6 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 18 residues within 4Å: Chain A: P.9, G.10, S.11, F.12, G.18, H.19, I.22, R.89, G.90, R.92, D.96, E.100, S.121, Y.125, I.128, S.129, S.130, S.131 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.11, A:S.11, A:F.12, A:H.19, A:R.89, A:G.90, A:R.92, A:I.128, A:S.130, A:S.131, A:S.131 Water bridges: A:R.89 Salt bridges: A:H.19, A:H.19, A:R.92 AGS.3: 17 residues within 4Å: Chain A: R.102 Chain B: P.9, G.10, S.11, F.12, G.18, H.19, I.22, R.89, G.90, R.92, S.121, Y.125, I.128, S.129, S.130, S.131 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:S.11, B:S.11, B:F.12, B:R.89, B:G.90, B:R.92, B:Y.125, B:S.130, B:S.131, B:S.131, B:S.131 Water bridges: B:D.13, B:R.89, B:R.89, B:R.89 Salt bridges: B:H.19, B:R.92 pi-Cation interactions: B:R.92 AGS.4: 16 residues within 4Å: Chain C: P.9, G.10, S.11, F.12, G.18, H.19, I.22, R.89, G.90, R.92, S.121, Y.125, I.128, S.129, S.130, S.131 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:S.11, C:F.12, C:R.89, C:G.90, C:R.92, C:Y.125, C:S.130, C:S.131, C:S.131 Water bridges: C:S.130 Salt bridges: C:H.19, C:H.19, C:R.92 pi-Cation interactions: C:R.92 AGS.5: 18 residues within 4Å: Chain D: P.9, G.10, S.11, F.12, G.18, H.19, I.22, R.89, G.90, R.92, D.96, E.100, S.121, Y.125, I.128, S.129, S.130, S.131 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:S.11, D:S.11, D:F.12, D:R.89, D:G.90, D:R.92, D:E.100, D:I.128, D:S.130, D:S.131, D:S.131 Water bridges: D:R.89 Salt bridges: D:H.19, D:H.19, D:R.92 AGS.7: 17 residues within 4Å: Chain D: R.102 Chain E: P.9, G.10, S.11, F.12, G.18, H.19, I.22, R.89, G.90, R.92, S.121, Y.125, I.128, S.129, S.130, S.131 19 PLIP interactions: 19 interactions with chain E Hydrogen bonds: E:S.11, E:S.11, E:F.12, E:H.19, E:R.89, E:G.90, E:R.92, E:Y.125, E:S.130, E:S.131, E:S.131, E:S.131 Water bridges: E:D.13, E:R.89, E:R.89, E:R.89 Salt bridges: E:H.19, E:R.92 pi-Cation interactions: E:R.92 AGS.8: 16 residues within 4Å: Chain F: P.9, G.10, S.11, F.12, G.18, H.19, I.22, R.89, G.90, R.92, S.121, Y.125, I.128, S.129, S.130, S.131 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:S.11, F:F.12, F:H.19, F:R.89, F:G.90, F:R.92, F:Y.125, F:S.130, F:S.131, F:S.131 Water bridges: F:S.130 Salt bridges: F:H.19, F:H.19, F:R.92 pi-Cation interactions: F:R.92

2 x 2W3: 2-[2-[(1S,2S)-2-[(3,4-dichlorophenyl)methylcarbamoyl]cyclohexyl]-6-ethyl-pyrimidin-4-yl]-4-oxidanyl-6-oxidanylidene-1H-pyrimidine-5-carboxamide(Non-covalent)

2W3.2: 17 residues within 4Å: Chain A: P.9, C.36, L.38, S.41, K.43, F.71, G.73, L.74, L.75, R.89, Y.99, E.100, L.103, M.106, N.107 Chain B: E.135, Y.139 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.9, A:L.38, A:L.38, A:L.74, A:L.75, A:L.103, A:M.106 Hydrogen bonds: A:S.41, A:S.41, A:K.43, A:L.75, A:Y.99, A:Y.99, B:E.135 Water bridges: A:N.107 Halogen bonds: A:C.36 2W3.6: 17 residues within 4Å: Chain D: P.9, C.36, L.38, S.41, K.43, F.71, G.73, L.74, L.75, R.89, Y.99, E.100, L.103, M.106, N.107 Chain E: E.135, Y.139 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:P.9, D:L.38, D:L.38, D:L.74, D:L.75, D:L.103, D:M.106 Hydrogen bonds: D:S.41, D:S.41, D:K.43, D:L.75, D:Y.99, D:Y.99, E:E.135, E:Y.139 Water bridges: D:N.107 Halogen bonds: D:C.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Jonge, B.L. et al., Discovery of Inhibitors of 4'-Phosphopantetheine Adenylyltransferase (PPAT) To Validate PPAT as a Target for Antibacterial Therapy. Antimicrob.Agents Chemother. (2013)

Release Date

2014-03-12

Peptides

Phosphopantetheine adenylyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Phosphopantetheine adenylyltransferase

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