SMTL ID : 8fg8.1 (1 other biounit)

Catalytic domain of GtfB in complex with inhibitor 2-[(2,4,5-Trihydroxyphenyl)methylidene]-1-benzofuran-3-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.215, D.221, N.265, D.743 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.215, A:E.215, A:D.221, A:N.265, H2O.1

1 x XV5: (2Z)-2-[(2,4,5-trihydroxyphenyl)methylidene]-1-benzofuran-3(2H)-one(Non-covalent)

XV5.2: 7 residues within 4Å: Chain A: L.217, N.265, E.299, W.301, R.324, D.372 Ligands: BTB.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.301 Hydrogen bonds: A:N.265, A:D.372

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.3: 14 residues within 4Å: Chain A: L.218, R.259, D.261, E.299, H.371, D.372, Q.376, N.646, F.691, D.693, N.698, Y.700, Q.744 Ligands: XV5.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.259, A:R.259, A:E.299, A:Q.376, A:N.646, A:N.698, A:Q.744, A:Q.744 Water bridges: A:D.693, A:D.693 Salt bridges: A:D.261, A:E.299, A:D.372, A:D.693

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

SO4.4: 4 residues within 4Å: Chain A: V.822, K.823, K.830, Y.831 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.831, A:Y.831 Water bridges: A:Q.826 Salt bridges: A:K.830 SO4.5: 2 residues within 4Å: Chain A: R.380, K.384 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.380, A:K.384 SO4.6: 2 residues within 4Å: Chain A: K.653, K.654 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.654 Salt bridges: A:K.654 SO4.7: 4 residues within 4Å: Chain A: T.555, D.556, N.557, G.558 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.557, A:N.557, A:G.558 Water bridges: A:D.556 SO4.8: 3 residues within 4Å: Chain A: A.414, T.415, E.416 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.415, A:T.415, A:E.416 SO4.9: 2 residues within 4Å: Chain A: R.482, N.538 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.538 Salt bridges: A:R.482 SO4.10: 3 residues within 4Å: Chain A: E.53, K.149, R.840 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.53 Salt bridges: A:K.149, A:R.840 SO4.11: 1 residues within 4Å: Chain A: R.513 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.513 SO4.12: 1 residues within 4Å: Chain A: R.809 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.279, A:R.809 SO4.13: 6 residues within 4Å: Chain A: H.238, N.242, Y.277, A.281, K.802, Y.803 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.242, A:N.242, A:Y.277, A:Y.803 Salt bridges: A:H.238, A:K.802

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahirwar, P. et al., Hydrogel-Encapsulated Biofilm Inhibitors Abrogate the Cariogenic Activity of Streptococcus mutans . J.Med.Chem. (2023)

Release Date

2023-06-14

Peptides

Glucosyltransferase-I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glucosyltransferase-I

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