SMTL ID : 1xc6.1

Native Structure Of Beta-Galactosidase from Penicillium sp. in complex with Galactose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 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: 12 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: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-BMA.2, EDO.66 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: 21 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 Ligands: NAG-NAG-BMA.1, IOD.13, IOD.47, IOD.61 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.534 Water bridges: A:T.336, A:S.341, A:N.535, A:N.535, A:N.531, A:K.563 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: 8 residues within 4Å: Chain A: N.651, R.694, N.723, K.752, N.753, Y.754, V.755 Ligands: IOD.50 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: 9 residues within 4Å: Chain A: A.670, H.671, S.672, Q.674, Q.709, N.736, N.738, N.740, Q.784 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Q.709, A:S.672 Hydrogen bonds: A:S.672, A:S.672, 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: 21 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.9, IOD.43, EDO.64 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.269, A:S.734, A:S.734 Hydrogen bonds: 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 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.416, A:N.416, A:N.416 NAG.7: 4 residues within 4Å: Chain A: R.114, Y.665, N.667 Ligands: IOD.57 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.667

1 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.8: 16 residues within 4Å: Chain A: Y.56, I.99, N.100, A.101, E.102, N.159, E.160, N.196, D.219, Y.221, F.225, E.259, F.265, Y.303, Y.323, Y.325 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.56, A:Y.56, A:N.100, A:A.101, A:N.159, A:E.160, A:N.196, A:D.219, A:Y.323, A:Y.325

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

NA.9: 3 residues within 4Å: Chain A: P.905, T.907 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.905

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

PO4.10: 5 residues within 4Å: Chain A: T.659, S.660, D.662, H.663, Y.684 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.660 Water bridges: A:S.660, A:S.660 Salt bridges: A:H.663

52 x IOD: IODIDE ION(Non-functional Binders)

IOD.11: 2 residues within 4Å: Chain A: F.273, Y.320 Ligand excluded by PLIP IOD.12: 4 residues within 4Å: Chain A: N.281, H.282, E.338, K.339 Ligand excluded by PLIP IOD.13: 6 residues within 4Å: Chain A: R.337, E.338 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-BMA.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-BMA.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-BMA.2, IOD.47 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain A: H.203, N.204 Ligand excluded by PLIP IOD.15: 1 residues within 4Å: Chain A: L.673 Ligand excluded by PLIP IOD.16: 1 residues within 4Å: Chain A: S.220 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain A: N.371, Y.406, S.425 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain A: T.652, Y.653 Ligand excluded by PLIP IOD.19: 3 residues within 4Å: Chain A: L.847, T.848 Ligands: IOD.55 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain A: G.473, V.511 Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain A: A.883, A.936, K.937 Ligand excluded by PLIP IOD.22: 3 residues within 4Å: Chain A: Q.3, K.4, Y.5 Ligand excluded by PLIP IOD.23: 1 residues within 4Å: Chain A: S.481 Ligand excluded by PLIP IOD.24: 4 residues within 4Å: Chain A: Q.78, K.85, A.144 Ligands: IOD.48 Ligand excluded by PLIP IOD.25: 2 residues within 4Å: Chain A: A.83, E.86 Ligand excluded by PLIP IOD.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.27: 2 residues within 4Å: Chain A: Q.832, W.923 Ligand excluded by PLIP IOD.28: 2 residues within 4Å: Chain A: H.696, K.798 Ligand excluded by PLIP IOD.29: 2 residues within 4Å: Chain A: R.809, K.968 Ligand excluded by PLIP IOD.30: 2 residues within 4Å: Chain A: P.589, S.622 Ligand excluded by PLIP IOD.31: 2 residues within 4Å: Chain A: H.671, K.711 Ligand excluded by PLIP IOD.32: 2 residues within 4Å: Chain A: F.707, T.742 Ligand excluded by PLIP IOD.33: 3 residues within 4Å: Chain A: Q.519, K.524, K.615 Ligand excluded by PLIP IOD.34: 4 residues within 4Å: Chain A: G.876, N.877, S.878, D.939 Ligand excluded by PLIP IOD.35: 1 residues within 4Å: Chain A: N.605 Ligand excluded by PLIP IOD.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.37: 3 residues within 4Å: Chain A: E.124, A.125, K.128 Ligand excluded by PLIP IOD.38: 1 residues within 4Å: Chain A: Q.610 Ligand excluded by PLIP IOD.39: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.40: 2 residues within 4Å: Chain A: G.224, F.225 Ligand excluded by PLIP IOD.41: 2 residues within 4Å: Chain A: F.859, D.860 Ligand excluded by PLIP IOD.42: 4 residues within 4Å: Chain A: N.917, Y.918, H.919, G.920 Ligand excluded by PLIP IOD.43: 4 residues within 4Å: Chain A: I.735 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.5, NAG-NAG-BMA-MAN-MAN-MAN-MAN.5, NAG-NAG-BMA-MAN-MAN-MAN-MAN.5 Ligand excluded by PLIP IOD.44: 3 residues within 4Å: Chain A: T.232, W.233, R.431 Ligand excluded by PLIP IOD.45: 1 residues within 4Å: Chain A: R.19 Ligand excluded by PLIP IOD.46: 6 residues within 4Å: Chain A: P.420, L.422, G.423, H.475, E.477, A.508 Ligand excluded by PLIP IOD.47: 4 residues within 4Å: Chain A: T.336, R.337 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-BMA.2, IOD.13 Ligand excluded by PLIP IOD.48: 3 residues within 4Å: Chain A: Q.78, K.143 Ligands: IOD.24 Ligand excluded by PLIP IOD.49: 4 residues within 4Å: Chain A: V.541, P.542, P.548, T.555 Ligand excluded by PLIP IOD.50: 3 residues within 4Å: Chain A: K.752, N.753 Ligands: NAG-NAG.3 Ligand excluded by PLIP IOD.51: 2 residues within 4Å: Chain A: S.634, E.942 Ligand excluded by PLIP IOD.52: 4 residues within 4Å: Chain A: R.515, L.528, Y.536, K.563 Ligand excluded by PLIP IOD.53: 3 residues within 4Å: Chain A: E.791, A.792, S.793 Ligand excluded by PLIP IOD.54: 1 residues within 4Å: Chain A: S.634 Ligand excluded by PLIP IOD.55: 2 residues within 4Å: Chain A: R.853 Ligands: IOD.19 Ligand excluded by PLIP IOD.56: 1 residues within 4Å: Chain A: K.963 Ligand excluded by PLIP IOD.57: 2 residues within 4Å: Chain A: R.114 Ligands: NAG.7 Ligand excluded by PLIP IOD.58: 1 residues within 4Å: Chain A: Y.964 Ligand excluded by PLIP IOD.59: 1 residues within 4Å: Chain A: T.147 Ligand excluded by PLIP IOD.60: 2 residues within 4Å: Chain A: N.229, S.231 Ligand excluded by PLIP IOD.61: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-BMA.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-BMA.2 Ligand excluded by PLIP IOD.62: 3 residues within 4Å: Chain A: E.463, Q.519, S.522 Ligand excluded by PLIP

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

EDO.63: 7 residues within 4Å: Chain A: L.20, M.21, A.350, K.351, S.353, P.354, Q.553 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.21 Water bridges: A:M.21, A:N.51, A:A.350, A:K.351 EDO.64: 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 No protein-ligand interaction detected (PLIP) EDO.65: 5 residues within 4Å: Chain A: N.535, A.564, T.587, T.588, P.589 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.535, A:T.587 Water bridges: A:N.535 EDO.66: 5 residues within 4Å: Chain A: Y.872, N.874, S.908, I.944 Ligands: NAG-NAG-BMA.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.874, A:S.908 EDO.67: 4 residues within 4Å: Chain A: E.10, H.246, E.247, P.361 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.246 Water bridges: A:H.243, A:E.247, A:Y.255 EDO.68: 5 residues within 4Å: Chain A: I.722, N.723, T.725, P.746, Y.754 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.722, A:T.725 Water bridges: A:E.724, A:T.725 EDO.69: 4 residues within 4Å: Chain A: T.240, T.244, D.363, L.364 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.364 Water bridges: A:T.240, A:G.362 EDO.70: 7 residues within 4Å: Chain A: N.310, N.313, L.314, G.315, Y.320, T.321, K.898 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.315 Water bridges: A:N.313, A:Q.895 EDO.71: 1 residues within 4Å: Chain A: D.173 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.122, A:S.122, A:D.173 EDO.72: 8 residues within 4Å: Chain A: S.353, P.354, G.355, S.388, F.390, D.439, Y.440, D.441 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.355, A:S.388, A:D.439, A:D.441 EDO.73: 5 residues within 4Å: Chain A: L.417, Q.421, L.448, V.501, A.504 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.421

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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