SMTL ID : 8fjc.2 (1 other biounit)

Structure of the catalytic domain of Streptococcus mutans GtfB complexed to acarbose in tetragonal space group P4322

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x GLC- GLC- AC1: 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose

GLC-GLC-AC1.1: 20 residues within 4Å: Chain A: L.166, Y.214, L.217, L.218, R.259, D.261, A.262, N.265, E.299, W.301, N.321, R.324, L.325, H.371, D.372, F.691, D.693, Y.700, V.741, Q.744 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.166 Hydrogen bonds: A:R.259, A:A.262, A:E.299, A:E.299, A:D.693, A:D.693, A:Q.744, A:Q.744, A:Y.214, A:Y.394, A:Y.394 Water bridges: A:N.698, A:N.698

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 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.4

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: R.615, A.670, G.673, V.674, K.732, G.733 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.615, A:R.615, A:A.670, A:G.673 EDO.4: 6 residues within 4Å: Chain A: G.340, M.341, N.342, N.483, E.490 Ligands: SO4.30 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.341, A:N.342, A:N.483, A:E.490 EDO.5: 5 residues within 4Å: Chain A: K.473, D.565, A.608, A.609, A.610 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.565 Water bridges: A:S.564, A:Q.566 EDO.6: 7 residues within 4Å: Chain A: N.184, S.185, N.186, Y.187, N.226, K.830, Y.831 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.185, A:N.186, A:N.226 EDO.7: 4 residues within 4Å: Chain A: I.401, D.450, F.647, Q.648 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.648 EDO.8: 4 residues within 4Å: Chain A: N.342, M.481, R.482, N.483 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.342, A:N.342, A:N.483

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

SO4.9: 2 residues within 4Å: Chain A: R.510, R.513 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: K.823, K.830, Y.831 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain A: R.482, N.538 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain A: R.380, K.384 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain A: K.289, A.617, A.618, R.638 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain A: N.254, K.282, H.294 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain A: K.279, R.809 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain A: E.53, K.149, R.840 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain A: G.451, Q.452, H.456 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain A: A.414, T.415, E.416 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain A: T.555, D.556, N.557 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain A: P.749, E.750, K.751 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain A: A.609, A.610 Ligand excluded by PLIP SO4.22: 6 residues within 4Å: Chain A: R.204, Y.205, Q.272, Y.308, D.311, D.312 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain A: K.653, K.654, E.655 Ligand excluded by PLIP SO4.24: 1 residues within 4Å: Chain A: R.91 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain A: K.530, A.531 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain A: R.380, V.391, V.392, G.393 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain A: P.334, N.336, Q.337 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain A: D.509, R.510 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain A: K.499, D.509, T.511 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain A: N.342, P.343, T.346 Ligands: EDO.4 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain A: D.354, D.355, N.356, A.357 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain A: V.616, A.617 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain A: N.136, T.137 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schormann, N. et al., The catalytic domains of Streptococcus mutans glucosyltransferases: a structural analysis. Acta Crystallogr.,Sect.F (2023)

Release Date

2023-05-17

Peptides

Glucosyltransferase-I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Glucosyltransferase-I

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