SMTL ID : 1tg7.1

Native structure of beta-galactosidase from Penicillium sp.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 11 residues within 4Å: Chain A: F.273, A.274, D.324, S.330, S.332, N.334, R.337, Y.872, T.946, T.947 Ligands: EDO.18 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.275, A:A.274 Hydrophobic interactions: A:F.273 Hydrogen bonds: A:R.337

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- BMA: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-BMA.2: 17 residues within 4Å: Chain A: H.282, E.283, R.286, T.336, E.338, S.341, S.429, P.472, T.513, D.529, N.531, S.532, Y.534, N.535, Y.566, N.585, T.947 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.534 Water bridges: A:T.336, A:E.338, A:S.341, A:S.341, A:N.535, A:N.535, A:N.535 Hydrogen bonds: A:D.529, A:N.535

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 7 residues within 4Å: Chain A: N.651, R.694, H.696, N.723, K.752, N.753, V.755 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.753

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.4: 8 residues within 4Å: Chain A: A.670, H.671, S.672, Q.674, Q.709, N.738, N.740, Q.784 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Q.674, A:Q.674, A:A.670, A:S.672, A:S.672 Hydrogen bonds: A:S.672

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.5: 22 residues within 4Å: Chain A: G.269, T.733, S.734, I.735, N.736, N.877, T.879, S.880, P.882, Y.899, V.900, N.901, N.902, I.903, G.904, P.905, Q.906, T.907 Ligands: NA.8, NA.10, PO4.12, EDO.16 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.734, A:S.734 Hydrogen bonds: A:S.734, A:S.734, A:G.269

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6: 2 residues within 4Å: Chain A: T.368, N.416 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.369, A:N.416 NAG.7: 3 residues within 4Å: Chain A: R.114, Y.665, N.667 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.667

3 x NA: SODIUM ION(Non-functional Binders)

NA.8: 3 residues within 4Å: Chain A: N.877, T.879 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.877 NA.9: 2 residues within 4Å: Chain A: K.459, A.557 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.459 Water bridges: A:K.459 NA.10: 3 residues within 4Å: Chain A: P.905, T.907 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.905 Water bridges: A:N.877

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.11: 5 residues within 4Å: Chain A: H.316, P.317, G.318, D.766, E.767 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.318, A:D.766, A:E.767, A:E.767 Water bridges: A:H.316, A:T.714, A:E.767 Salt bridges: A:H.316 PO4.12: 5 residues within 4Å: Chain A: W.730, N.739, N.740, A.741 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.739, A:N.739, A:N.740 Water bridges: A:T.742 PO4.13: 5 residues within 4Å: Chain A: T.659, S.660, D.662, H.663, Y.684 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.660 Water bridges: A:S.660, A:S.660, A:D.662, A:D.662, A:H.663 Salt bridges: A:H.663 PO4.14: 3 residues within 4Å: Chain A: S.634, K.636, E.942 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.634, A:E.942 Water bridges: A:P.633, A:L.635, A:K.636, A:L.943 Salt bridges: A:K.636

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

EDO.15: 7 residues within 4Å: Chain A: L.20, M.21, A.350, K.351, S.353, P.354, L.357 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:M.21, A:S.353 Water bridges: A:M.21, A:N.51, A:A.350, A:K.351 EDO.16: 6 residues within 4Å: Chain A: P.267, W.268, G.269, S.734, I.735 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.226, A:G.269 EDO.17: 6 residues within 4Å: Chain A: N.535, A.564, G.565, T.587, T.588, P.589 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.535, A:N.535, A:T.587 EDO.18: 5 residues within 4Å: Chain A: Y.872, N.874, S.908, I.944 Ligands: NAG-NAG-BMA.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.874, A:S.908 Water bridges: A:S.908 EDO.19: 4 residues within 4Å: Chain A: E.10, H.246, E.247, P.361 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.246 Water bridges: A:E.10, A:H.243, A:E.247, A:P.251, A:Y.255 EDO.20: 5 residues within 4Å: Chain A: I.722, N.723, T.725, P.746, Y.754 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.722, A:T.725 Water bridges: A:T.725 EDO.21: 5 residues within 4Å: Chain A: T.240, T.244, G.362, D.363, L.364 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.364 Water bridges: A:T.240, A:H.243, A:T.244, A:T.244, A:G.362 EDO.22: 8 residues within 4Å: Chain A: N.100, E.102, Y.221, F.225, F.265, Y.303, Y.325 Ligands: EDO.23 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.100, A:Y.323, A:Y.325, A:Y.325 EDO.23: 11 residues within 4Å: Chain A: Y.56, I.99, N.100, A.101, N.159, E.160, N.196, D.219, E.259, Y.303 Ligands: EDO.22 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.56, A:I.99, A:N.100, A:A.101, A:N.159, A:N.196, A:D.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rojas, A.L. et al., Crystal Structures of beta-Galactosidase from Penicillium sp. and its Complex with Galactose. J.Mol.Biol. (2004)

Release Date

2004-11-02

Peptides

beta-galactosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

beta-galactosidase

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