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

Crystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with (R)-3-(3-chlorophenyl)-3-((5-methyl-7-oxo-4,7-dihydro-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)amino)propanenitrile

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-hexamer

Ligands

6 x EXJ: (3R)-3-(3-chlorophenyl)-3-[(5-methyl-7-oxo-6,7-dihydro[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)amino]propanenitrile(Non-covalent)

EXJ.1: 17 residues within 4Å: Chain A: P.8, G.9, T.10, A.37, A.38, S.39, F.70, S.71, D.72, L.73, M.74, L.102, M.105, N.106 Chain C: E.134, V.135, H.138 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:A.37, A:F.70, A:F.70, A:M.105, C:V.135 Hydrogen bonds: A:S.39, A:D.72, A:M.74 Water bridges: A:A.75, A:Y.98, C:E.134 EXJ.5: 17 residues within 4Å: Chain B: P.8, G.9, T.10, A.37, A.38, S.39, P.40, F.70, S.71, D.72, L.73, M.74, L.102, M.105, N.106 Chain F: V.135, H.138 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain F Hydrophobic interactions: B:T.10, B:A.37, B:F.70, B:F.70, F:V.135 Hydrogen bonds: B:S.39, B:D.72, B:M.74 Water bridges: B:A.75, F:E.134 pi-Stacking: F:H.138 EXJ.9: 17 residues within 4Å: Chain C: P.8, G.9, T.10, A.37, A.38, S.39, F.70, S.71, D.72, L.73, M.74, L.102, M.105, N.106 Chain E: E.134, V.135, H.138 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:A.37, C:F.70, C:F.70, C:M.105, E:V.135 Hydrogen bonds: C:S.39, C:D.72, C:M.74 Water bridges: C:A.75, C:Y.98 EXJ.13: 17 residues within 4Å: Chain B: V.135, H.138 Chain D: P.8, G.9, T.10, A.37, A.38, S.39, P.40, F.70, S.71, D.72, L.73, M.74, L.102, M.105, N.106 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain D Hydrophobic interactions: B:V.135, D:T.10, D:A.37, D:F.70, D:F.70 pi-Stacking: B:H.138 Hydrogen bonds: D:S.39, D:D.72, D:M.74 Water bridges: D:A.75 EXJ.17: 17 residues within 4Å: Chain A: E.134, V.135, H.138 Chain E: P.8, G.9, T.10, A.37, A.38, S.39, F.70, S.71, D.72, L.73, M.74, L.102, M.105, N.106 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:A.37, E:F.70, E:F.70, E:M.105, A:V.135 Hydrogen bonds: E:S.39, E:D.72, E:M.74 Water bridges: E:A.75 EXJ.21: 17 residues within 4Å: Chain D: V.135, H.138 Chain F: P.8, G.9, T.10, A.37, A.38, S.39, P.40, F.70, S.71, D.72, L.73, M.74, L.102, M.105, N.106 12 PLIP interactions: 3 interactions with chain D, 9 interactions with chain F Hydrophobic interactions: D:V.135, F:T.10, F:A.37, F:F.70, F:F.70 Water bridges: D:E.134, F:A.75, F:Y.98 pi-Stacking: D:H.138 Hydrogen bonds: F:S.39, F:D.72, F:M.74

6 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 20 residues within 4Å: Chain A: Y.7, P.8, G.9, T.10, F.11, G.17, H.18, I.21, R.88, G.89, R.91, D.95, E.99, P.120, W.124, I.127, S.128, S.129, S.130 Ligands: MG.3 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:Y.7, A:T.10, A:F.11, A:R.88, A:G.89, A:R.91, A:E.99, A:W.124, A:S.129, A:S.130, A:S.130 Water bridges: A:T.15, A:R.88, A:R.88, A:S.129, A:S.129 Salt bridges: A:H.18, A:H.18, A:R.91 pi-Cation interactions: A:R.91 ATP.6: 18 residues within 4Å: Chain B: Y.7, P.8, G.9, T.10, F.11, G.17, H.18, I.21, R.88, G.89, R.91, P.120, W.124, I.127, S.128, S.129, S.130 Ligands: MG.7 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:Y.7, B:T.10, B:T.10, B:F.11, B:R.88, B:G.89, B:R.91, B:W.124, B:S.129, B:S.130, B:S.130 Water bridges: B:T.15, B:R.88, B:R.88, B:R.88, B:S.129, B:S.129, B:K.133 Salt bridges: B:H.18, B:H.18, B:R.91 pi-Cation interactions: B:R.91 ATP.10: 20 residues within 4Å: Chain C: Y.7, P.8, G.9, T.10, F.11, G.17, H.18, I.21, R.88, G.89, R.91, D.95, E.99, P.120, W.124, I.127, S.128, S.129, S.130 Ligands: MG.11 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:T.10, C:F.11, C:R.88, C:G.89, C:R.91, C:E.99, C:E.99, C:W.124, C:S.129, C:S.130, C:S.130 Water bridges: C:T.10, C:R.88, C:R.88, C:S.129, C:S.129 Salt bridges: C:H.18, C:H.18, C:R.91 pi-Cation interactions: C:R.91 ATP.14: 18 residues within 4Å: Chain D: Y.7, P.8, G.9, T.10, F.11, G.17, H.18, I.21, R.88, G.89, R.91, P.120, W.124, I.127, S.128, S.129, S.130 Ligands: MG.15 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:T.10, D:T.10, D:T.10, D:F.11, D:R.88, D:G.89, D:R.91, D:W.124, D:S.129, D:S.130, D:S.130 Water bridges: D:R.88, D:R.88, D:R.88, D:S.129, D:S.129, D:K.133 Salt bridges: D:H.18, D:H.18, D:R.91 pi-Cation interactions: D:R.91 ATP.18: 20 residues within 4Å: Chain E: Y.7, P.8, G.9, T.10, F.11, G.17, H.18, I.21, R.88, G.89, R.91, D.95, E.99, P.120, W.124, I.127, S.128, S.129, S.130 Ligands: MG.19 18 PLIP interactions: 18 interactions with chain E Hydrogen bonds: E:T.10, E:F.11, E:R.88, E:G.89, E:R.91, E:E.99, E:W.124, E:S.129, E:S.130, E:S.130 Water bridges: E:R.88, E:R.88, E:S.129, E:S.129 Salt bridges: E:H.18, E:H.18, E:R.91 pi-Cation interactions: E:R.91 ATP.22: 18 residues within 4Å: Chain F: Y.7, P.8, G.9, T.10, F.11, G.17, H.18, I.21, R.88, G.89, R.91, P.120, W.124, I.127, S.128, S.129, S.130 Ligands: MG.23 22 PLIP interactions: 22 interactions with chain F Hydrogen bonds: F:Y.7, F:T.10, F:T.10, F:F.11, F:R.88, F:G.89, F:R.91, F:W.124, F:S.129, F:S.130, F:S.130 Water bridges: F:T.15, F:R.88, F:R.88, F:R.88, F:S.129, F:S.129, F:K.133 Salt bridges: F:H.18, F:H.18, F:R.91 pi-Cation interactions: F:R.91

6 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 1 residues within 4Å: Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: ATP.6 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Ligands: ATP.10 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Ligands: ATP.14 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Ligands: ATP.18 No protein-ligand interaction detected (PLIP) MG.23: 1 residues within 4Å: Ligands: ATP.22 No protein-ligand interaction detected (PLIP)

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: S.121, K.122 Chain B: H.104, R.107 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Water bridges: B:H.104, B:H.104, A:S.121, A:E.123, A:E.123 Salt bridges: B:H.104, B:R.107, A:K.122 Hydrogen bonds: A:S.121, A:K.122 SO4.8: 4 residues within 4Å: Chain A: H.104, R.107 Chain B: S.121, K.122 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:K.122 Water bridges: B:R.24, B:S.121, B:E.123, A:H.104, A:H.104 Salt bridges: B:K.122, A:H.104, A:R.107 SO4.12: 4 residues within 4Å: Chain C: S.121, K.122 Chain D: H.104, R.107 10 PLIP interactions: 3 interactions with chain D, 7 interactions with chain C Water bridges: D:H.104, C:S.121, C:K.122, C:E.123, C:E.123 Salt bridges: D:H.104, D:R.107, C:K.122 Hydrogen bonds: C:S.121, C:K.122 SO4.16: 4 residues within 4Å: Chain C: H.104, R.107 Chain D: S.121, K.122 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:K.122 Water bridges: D:R.24, D:S.121, D:K.122, D:E.123, C:H.104 Salt bridges: D:K.122, C:H.104, C:R.107 SO4.20: 4 residues within 4Å: Chain E: S.121, K.122 Chain F: H.104, R.107 10 PLIP interactions: 7 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:S.121, E:K.122 Water bridges: E:S.121, E:K.122, E:E.123, E:E.123, F:H.104 Salt bridges: E:K.122, F:H.104, F:R.107 SO4.24: 4 residues within 4Å: Chain E: H.104, R.107 Chain F: S.121, K.122 9 PLIP interactions: 4 interactions with chain E, 5 interactions with chain F Water bridges: E:H.104, E:H.104, F:R.24, F:S.121, F:E.123 Salt bridges: E:H.104, E:R.107, F:K.122 Hydrogen bonds: F:K.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moreau, R.J. et al., Fragment-Based Drug Discovery of Inhibitors of Phosphopantetheine Adenylyltransferase from Gram-Negative Bacteria. J. Med. Chem. (2018)

Release Date

2018-03-14

Peptides

Phosphopantetheine adenylyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Phosphopantetheine adenylyltransferase

Related Entries With Identical Sequence