SMTL ID : 6b7c.2 (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-dimer

Ligands

2 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: 10 residues within 4Å: Chain A: G.9, A.37, F.70, D.72, L.73, M.74, L.102, M.105, N.106 Ligands: DMS.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.37, A:F.70 Hydrogen bonds: A:D.72, A:M.74 Water bridges: A:A.75 CWP.7: 13 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 Ligands: SO4.8, DMS.13 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.8, B:A.37, B:F.70, B:L.102, B:M.105 Hydrogen bonds: B:D.72, B:M.74

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

SO4.2: 4 residues within 4Å: Chain A: S.121, K.122 Chain B: H.104, R.107 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.122 Water bridges: A:R.24, A:S.121, A:K.122, A:E.123, B:H.104, B:H.104 Salt bridges: A:K.122, B:H.104, B:R.107 SO4.3: 2 residues within 4Å: Chain A: E.134, H.138 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.134 Salt bridges: A:H.138 SO4.8: 4 residues within 4Å: Chain B: S.39, P.40, S.41 Ligands: CWP.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.41, B:S.41, B:S.41 Water bridges: B:S.39 SO4.9: 4 residues within 4Å: Chain A: H.104, R.107 Chain B: S.121, K.122 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Salt bridges: A:H.104, A:R.107, B:K.122 Hydrogen bonds: B:S.121, B:K.122 Water bridges: B:R.24, B:E.123

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

PEG.4: 3 residues within 4Å: Chain A: R.4, Q.81, H.82 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.82 PEG.10: 3 residues within 4Å: Chain B: N.16, D.20, W.124 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.20 Water bridges: B:N.16, B:S.121 PEG.11: 2 residues within 4Å: Chain B: R.4, H.82 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.82

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

POP.5: 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:Y.7, A:T.10, A:R.88, A:I.127, A:S.129, A:S.129, A:S.130, A:S.130 Salt bridges: A:H.18, A:H.18 POP.12: 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:H.18, B:R.88, B:S.128, B:S.129, B:S.129, B:S.130 Salt bridges: B:H.18, B:H.18

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

DMS.6: 3 residues within 4Å: Chain A: M.74, Y.98 Ligands: CWP.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.88 DMS.13: 6 residues within 4Å: Chain B: K.42, M.74, R.88, Y.98, L.102 Ligands: CWP.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.88, B:R.88 DMS.14: 7 residues within 4Å: Chain A: Q.2 Chain B: T.26, Q.27, M.28, F.29, D.30, N.64 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:D.30 Salt bridges: B:D.30 Hydrogen bonds: A:Q.2

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phosphopantetheine adenylyltransferase

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