SMTL ID : 6b7c.4 (3 other biounits)

Crystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with N-((1,3-dimethyl-1H-pyrazol-5-yl)methyl)-5-methyl-1H-imidazo[4,5-b]pyridin-2-amine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-trimer

Ligands

3 x CWP: N-[(1,3-dimethyl-1H-pyrazol-5-yl)methyl]-5-methyl-3H-imidazo[4,5-b]pyridin-2-amine(Non-covalent)

CWP.1: 17 residues within 4Å: Chain A: P.8, G.9, A.37, S.39, F.70, D.72, L.73, M.74, L.102, M.105, N.106 Chain B: L.131, E.134, V.135, H.138 Ligands: SO4.2, DMS.7 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.8, A:A.37, A:F.70, A:L.102, A:M.105, B:L.131, B:E.134 Hydrogen bonds: A:D.72, A:M.74 CWP.9: 17 residues within 4Å: Chain B: P.8, G.9, A.37, S.39, F.70, D.72, L.73, M.74, L.102, M.105, N.106 Chain C: L.131, E.134, V.135, H.138 Ligands: SO4.10, DMS.15 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:P.8, B:A.37, B:F.70, B:L.102, B:M.105, C:L.131, C:E.134 Hydrogen bonds: B:D.72, B:M.74 Water bridges: B:T.10 CWP.17: 17 residues within 4Å: Chain A: L.131, E.134, V.135, H.138 Chain C: P.8, G.9, A.37, S.39, F.70, D.72, L.73, M.74, L.102, M.105, N.106 Ligands: SO4.18, DMS.23 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:P.8, C:A.37, C:F.70, C:L.102, C:M.105, A:L.131, A:E.134 Hydrogen bonds: C:D.72, C:M.74

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

SO4.2: 6 residues within 4Å: Chain A: S.39, P.40, S.41 Chain B: R.137, H.138 Ligands: CWP.1 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Water bridges: B:E.134, A:S.39 Salt bridges: B:R.137, B:H.138 Hydrogen bonds: A:S.41, A:S.41, A:S.41 SO4.3: 2 residues within 4Å: Chain A: S.121, K.122 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.121, A:K.122 Water bridges: A:R.24, A:E.123 Salt bridges: A:K.122 SO4.10: 6 residues within 4Å: Chain B: S.39, P.40, S.41 Chain C: R.137, H.138 Ligands: CWP.9 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain B Salt bridges: C:R.137, C:H.138 Hydrogen bonds: B:S.41, B:S.41, B:S.41 Water bridges: B:S.39 SO4.11: 2 residues within 4Å: Chain B: S.121, K.122 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.121, B:K.122 Water bridges: B:R.24, B:E.123 Salt bridges: B:K.122 SO4.18: 6 residues within 4Å: Chain A: R.137, H.138 Chain C: S.39, P.40, S.41 Ligands: CWP.17 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.41, C:S.41, C:S.41 Water bridges: C:S.39 Salt bridges: A:R.137, A:H.138 SO4.19: 2 residues within 4Å: Chain C: S.121, K.122 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.121, C:K.122 Water bridges: C:R.24, C:E.123 Salt bridges: C:K.122

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 3 residues within 4Å: Chain A: N.16, D.20, W.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.20 Water bridges: A:N.16, A:S.121 PEG.5: 2 residues within 4Å: Chain A: R.4, H.82 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.82 PEG.12: 3 residues within 4Å: Chain B: N.16, D.20, W.124 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.16, B:S.121 PEG.13: 2 residues within 4Å: Chain B: R.4, H.82 No protein-ligand interaction detected (PLIP) PEG.20: 3 residues within 4Å: Chain C: N.16, D.20, W.124 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.16, C:S.121 PEG.21: 2 residues within 4Å: Chain C: R.4, H.82 No protein-ligand interaction detected (PLIP)

3 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.6: 6 residues within 4Å: Chain A: G.9, T.10, F.11, H.18, S.128, S.129 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.10, A:F.11, A:S.129 Water bridges: A:T.10, A:H.18, A:H.18, A:R.88, A:S.128, A:S.129, A:S.129, A:S.130 Salt bridges: A:H.18, A:H.18 POP.14: 6 residues within 4Å: Chain B: G.9, T.10, F.11, H.18, S.128, S.129 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:T.10, B:F.11, B:S.129 Water bridges: B:T.10, B:H.18, B:R.88, B:I.127, B:S.128, B:S.129, B:S.129, B:S.130 Salt bridges: B:H.18, B:H.18 POP.22: 6 residues within 4Å: Chain C: G.9, T.10, F.11, H.18, S.128, S.129 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:T.10, C:F.11, C:S.129 Water bridges: C:T.10, C:H.18, C:H.18, C:R.88, C:S.128, C:S.129, C:S.129, C:S.130 Salt bridges: C:H.18, C:H.18

6 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 7 residues within 4Å: Chain A: K.42, M.74, R.88, Y.98, L.102 Chain B: E.134 Ligands: CWP.1 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.88, A:R.88 Salt bridges: B:E.134 DMS.8: 6 residues within 4Å: Chain A: T.26, Q.27, M.28, F.29, D.30, N.64 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.30 Salt bridges: A:D.30 DMS.15: 7 residues within 4Å: Chain B: K.42, M.74, R.88, Y.98, L.102 Chain C: E.134 Ligands: CWP.9 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.88, B:R.88 Salt bridges: C:E.134 DMS.16: 6 residues within 4Å: Chain B: T.26, Q.27, M.28, F.29, D.30, N.64 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.30 Salt bridges: B:D.30 DMS.23: 7 residues within 4Å: Chain A: E.134 Chain C: K.42, M.74, R.88, Y.98, L.102 Ligands: CWP.17 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.88, C:R.88 Salt bridges: A:E.134 DMS.24: 6 residues within 4Å: Chain C: T.26, Q.27, M.28, F.29, D.30, N.64 2 PLIP interactions: 2 interactions with chain C Water bridges: C:D.30 Salt bridges: C:D.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Proudfoot, A. et al., High-Confidence Protein-Ligand Complex Modeling by NMR-Guided Docking Enables Early Hit Optimization. J. Am. Chem. Soc. (2017)

Release Date

2017-12-27

Peptides

Phosphopantetheine adenylyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

Phosphopantetheine adenylyltransferase

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