SMTL ID : 6b7e.2 (4 other biounits)

Crystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with (R)-4-(5-(difluoromethyl)-1H-imidazol-1-yl)-3,3-dimethylisochroman-1-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: S.121, K.122 Chain B: H.104, R.107 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.24, A:K.122 Salt bridges: A:K.122, B:H.104, B:R.107 Water bridges: B:H.104, B:H.104 SO4.2: 4 residues within 4Å: Chain A: H.18, R.91, S.128, S.129 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.129 Water bridges: A:S.129, A:S.130 Salt bridges: A:H.18, A:R.91 SO4.3: 2 residues within 4Å: Chain A: L.73, L.102 No protein-ligand interaction detected (PLIP) SO4.6: 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:S.121, B:K.122 Water bridges: B:E.123, B:E.123, A:H.104, A:H.104 Salt bridges: B:K.122, A:H.104, A:R.107 SO4.7: 4 residues within 4Å: Chain B: S.39, P.40, S.41 Ligands: CWA.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.41, B:S.41 Water bridges: B:S.39 SO4.8: 4 residues within 4Å: Chain B: H.18, R.91, S.128, S.129 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.129 Water bridges: B:H.18, B:R.91, B:S.129, B:S.130, B:S.130 Salt bridges: B:H.18, B:R.91 SO4.9: 5 residues within 4Å: Chain B: G.9, T.10, K.42, R.88 Ligands: CWA.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.10 Water bridges: B:F.11 Salt bridges: B:R.88

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

DMS.4: 6 residues within 4Å: Chain A: T.26, Q.27, M.28, F.29, D.30 Chain B: K.3 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:D.30 Hydrogen bonds: B:K.3 DMS.10: 7 residues within 4Å: Chain A: Q.2, K.3 Chain B: T.26, Q.27, M.28, F.29, D.30 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:D.30

1 x CWA: (4R)-4-[5-(difluoromethyl)-1H-imidazol-1-yl]-3,3-dimethyl-3,4-dihydro-1H-2-benzopyran-1-one(Non-covalent)

CWA.5: 12 residues within 4Å: Chain B: P.8, G.9, A.37, F.70, L.73, M.74, R.88, Y.98, L.102, N.106 Ligands: SO4.7, SO4.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.37, B:F.70, B:L.102 Hydrogen bonds: B:M.74, B:N.106 Water bridges: B:A.75

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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