SMTL ID : 2xn2.1

Structure of alpha-galactosidase from Lactobacillus acidophilus NCFM with galactose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-tetramer

Ligands

4 x GLA: alpha-D-galactopyranose(Non-covalent)

GLA.1: 16 residues within 4Å: Chain A: W.340, F.345, D.370, D.371, R.377, W.415, R.447, K.480, D.482, N.484, C.530, G.532, G.533, W.549, D.552 Ligands: IMD.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:D.370, A:D.371, A:D.371, A:W.415, A:R.447, A:R.447, A:K.480, A:D.482, A:D.482, A:N.484, A:N.484, A:G.533, A:W.549, A:D.552 Water bridges: A:D.552 Salt bridges: A:R.447 GLA.28: 16 residues within 4Å: Chain B: W.340, F.345, D.370, D.371, R.377, W.415, R.447, K.480, D.482, N.484, C.530, G.532, G.533, W.549, D.552 Ligands: IMD.29 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:D.370, B:D.371, B:W.415, B:R.447, B:R.447, B:K.480, B:D.482, B:N.484, B:N.484, B:G.533, B:W.549, B:D.552 Salt bridges: B:R.447 GLA.55: 16 residues within 4Å: Chain C: W.340, F.345, D.370, D.371, R.377, W.415, R.447, K.480, D.482, N.484, C.530, G.532, G.533, W.549, D.552 Ligands: IMD.56 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:D.370, C:D.371, C:D.371, C:W.415, C:R.447, C:R.447, C:K.480, C:D.482, C:D.482, C:N.484, C:N.484, C:G.533, C:W.549, C:D.552 Water bridges: C:D.552 Salt bridges: C:R.447 GLA.82: 16 residues within 4Å: Chain D: W.340, F.345, D.370, D.371, R.377, W.415, R.447, K.480, D.482, N.484, C.530, G.532, G.533, W.549, D.552 Ligands: IMD.83 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:D.370, D:D.371, D:W.415, D:R.447, D:R.447, D:K.480, D:D.482, D:N.484, D:N.484, D:G.533, D:W.549, D:D.552 Salt bridges: D:R.447

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 9 residues within 4Å: Chain A: H.203, R.447, N.484, G.532, D.552 Chain C: G.58, F.59 Ligands: GLA.1, GOL.65 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Water bridges: C:F.59 Hydrogen bonds: A:N.484 IMD.29: 9 residues within 4Å: Chain B: H.203, R.447, N.484, G.532, D.552 Chain D: G.58, F.59 Ligands: GLA.28, GOL.92 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:N.484 Water bridges: D:F.59 IMD.56: 9 residues within 4Å: Chain A: G.58, F.59 Chain C: H.203, R.447, N.484, G.532, D.552 Ligands: GOL.11, GLA.55 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Water bridges: A:F.59 Hydrogen bonds: C:N.484 IMD.83: 9 residues within 4Å: Chain B: G.58, F.59 Chain D: H.203, R.447, N.484, G.532, D.552 Ligands: GOL.38, GLA.82 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:N.484 Water bridges: B:F.59

100 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: Y.282, S.488, I.490, Y.504 Chain C: A.83, G.84, E.85, M.86, D.87, F.88 Ligand excluded by PLIP GOL.4: 8 residues within 4Å: Chain A: H.36, L.37, Y.38, F.39, Y.189, V.190, K.192 Chain B: K.681 Ligand excluded by PLIP GOL.5: 9 residues within 4Å: Chain A: V.668, V.669, N.670, D.714, P.715, E.717, K.722, A.723, K.724 Ligand excluded by PLIP GOL.6: 9 residues within 4Å: Chain A: G.385, D.386, K.388, N.426, L.427, E.430, H.431, N.462, Q.466 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: K.457, R.460, D.461, F.464, D.513, L.514, K.517 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: K.7, D.9, N.12, V.14, H.16, N.45, Y.46 Ligand excluded by PLIP GOL.9: 8 residues within 4Å: Chain A: K.121, G.122, L.123, W.286, E.293, F.294, Q.295, L.509 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain A: R.441, K.442 Chain C: P.64, F.105, V.145 Ligand excluded by PLIP GOL.11: 9 residues within 4Å: Chain A: D.56, R.57, G.58 Chain B: A.675, Q.676 Chain C: H.203, A.204, Q.586 Ligands: IMD.56 Ligand excluded by PLIP GOL.12: 8 residues within 4Å: Chain A: A.497, D.498 Chain C: R.96, N.97, P.98, G.100, Y.178, K.285 Ligand excluded by PLIP GOL.13: 8 residues within 4Å: Chain A: I.197, V.209, R.211, T.243, N.244, E.245, L.308, Y.564 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain A: S.659, N.660, K.661, D.688, K.691 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain A: N.695, F.702, F.712, Y.726, F.728 Chain B: Q.49 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain A: L.495, P.496, Q.499, R.506 Ligand excluded by PLIP GOL.17: 3 residues within 4Å: Chain A: W.340, Y.344, F.345 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain A: G.455, R.460, R.506, L.509, G.510 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain A: K.645, S.649, Q.651, T.680, K.681 Chain B: D.191 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain A: P.98, S.146, K.147, G.173, E.174, E.175 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain A: I.332, R.333, P.334, E.365, K.411, R.633 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain A: D.191, K.192, D.193, R.267, G.271 Chain B: Y.678 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain A: L.398, G.399, I.470, S.473, K.475, I.476 Ligands: GOL.24 Ligand excluded by PLIP GOL.24: 4 residues within 4Å: Chain A: K.469, D.472, S.473 Ligands: GOL.23 Ligand excluded by PLIP GOL.25: 4 residues within 4Å: Chain A: F.464, E.465, V.468, R.521 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain A: N.662, K.691, A.730, I.731, N.732 Ligand excluded by PLIP GOL.27: 11 residues within 4Å: Chain A: G.32, T.33, L.34, R.73, K.78, Y.80, S.81, E.85, L.106, A.107, L.141 Ligand excluded by PLIP GOL.30: 10 residues within 4Å: Chain B: Y.282, S.488, I.490, Y.504 Chain D: A.83, G.84, E.85, M.86, D.87, F.88 Ligand excluded by PLIP GOL.31: 8 residues within 4Å: Chain A: K.681 Chain B: H.36, L.37, Y.38, F.39, Y.189, V.190, K.192 Ligand excluded by PLIP GOL.32: 9 residues within 4Å: Chain B: V.668, V.669, N.670, D.714, P.715, E.717, K.722, A.723, K.724 Ligand excluded by PLIP GOL.33: 9 residues within 4Å: Chain B: G.385, D.386, K.388, N.426, L.427, E.430, H.431, N.462, Q.466 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain B: K.457, R.460, D.461, F.464, D.513, L.514, K.517 Ligand excluded by PLIP GOL.35: 7 residues within 4Å: Chain B: K.7, D.9, N.12, V.14, H.16, N.45, Y.46 Ligand excluded by PLIP GOL.36: 8 residues within 4Å: Chain B: K.121, G.122, L.123, W.286, E.293, F.294, Q.295, L.509 Ligand excluded by PLIP GOL.37: 5 residues within 4Å: Chain B: R.441, K.442 Chain D: P.64, F.105, V.145 Ligand excluded by PLIP GOL.38: 9 residues within 4Å: Chain A: A.675, Q.676 Chain B: D.56, R.57, G.58 Chain D: H.203, A.204, Q.586 Ligands: IMD.83 Ligand excluded by PLIP GOL.39: 8 residues within 4Å: Chain B: A.497, D.498 Chain D: R.96, N.97, P.98, G.100, Y.178, K.285 Ligand excluded by PLIP GOL.40: 8 residues within 4Å: Chain B: I.197, V.209, R.211, T.243, N.244, E.245, L.308, Y.564 Ligand excluded by PLIP GOL.41: 5 residues within 4Å: Chain B: S.659, N.660, K.661, D.688, K.691 Ligand excluded by PLIP GOL.42: 6 residues within 4Å: Chain A: Q.49 Chain B: N.695, F.702, F.712, Y.726, F.728 Ligand excluded by PLIP GOL.43: 4 residues within 4Å: Chain B: L.495, P.496, Q.499, R.506 Ligand excluded by PLIP GOL.44: 3 residues within 4Å: Chain B: W.340, Y.344, F.345 Ligand excluded by PLIP GOL.45: 5 residues within 4Å: Chain B: G.455, R.460, R.506, L.509, G.510 Ligand excluded by PLIP GOL.46: 6 residues within 4Å: Chain A: D.191 Chain B: K.645, S.649, Q.651, T.680, K.681 Ligand excluded by PLIP GOL.47: 6 residues within 4Å: Chain B: P.98, S.146, K.147, G.173, E.174, E.175 Ligand excluded by PLIP GOL.48: 6 residues within 4Å: Chain B: I.332, R.333, P.334, E.365, K.411, R.633 Ligand excluded by PLIP GOL.49: 6 residues within 4Å: Chain A: Y.678 Chain B: D.191, K.192, D.193, R.267, G.271 Ligand excluded by PLIP GOL.50: 7 residues within 4Å: Chain B: L.398, G.399, I.470, S.473, K.475, I.476 Ligands: GOL.51 Ligand excluded by PLIP GOL.51: 4 residues within 4Å: Chain B: K.469, D.472, S.473 Ligands: GOL.50 Ligand excluded by PLIP GOL.52: 4 residues within 4Å: Chain B: F.464, E.465, V.468, R.521 Ligand excluded by PLIP GOL.53: 5 residues within 4Å: Chain B: N.662, K.691, A.730, I.731, N.732 Ligand excluded by PLIP GOL.54: 11 residues within 4Å: Chain B: G.32, T.33, L.34, R.73, K.78, Y.80, S.81, E.85, L.106, A.107, L.141 Ligand excluded by PLIP GOL.57: 10 residues within 4Å: Chain A: A.83, G.84, E.85, M.86, D.87, F.88 Chain C: Y.282, S.488, I.490, Y.504 Ligand excluded by PLIP GOL.58: 8 residues within 4Å: Chain C: H.36, L.37, Y.38, F.39, Y.189, V.190, K.192 Chain D: K.681 Ligand excluded by PLIP GOL.59: 9 residues within 4Å: Chain C: V.668, V.669, N.670, D.714, P.715, E.717, K.722, A.723, K.724 Ligand excluded by PLIP GOL.60: 9 residues within 4Å: Chain C: G.385, D.386, K.388, N.426, L.427, E.430, H.431, N.462, Q.466 Ligand excluded by PLIP GOL.61: 7 residues within 4Å: Chain C: K.457, R.460, D.461, F.464, D.513, L.514, K.517 Ligand excluded by PLIP GOL.62: 7 residues within 4Å: Chain C: K.7, D.9, N.12, V.14, H.16, N.45, Y.46 Ligand excluded by PLIP GOL.63: 8 residues within 4Å: Chain C: K.121, G.122, L.123, W.286, E.293, F.294, Q.295, L.509 Ligand excluded by PLIP GOL.64: 5 residues within 4Å: Chain A: P.64, F.105, V.145 Chain C: R.441, K.442 Ligand excluded by PLIP GOL.65: 9 residues within 4Å: Chain A: H.203, A.204, Q.586 Chain C: D.56, R.57, G.58 Chain D: A.675, Q.676 Ligands: IMD.2 Ligand excluded by PLIP GOL.66: 8 residues within 4Å: Chain A: R.96, N.97, P.98, G.100, Y.178, K.285 Chain C: A.497, D.498 Ligand excluded by PLIP GOL.67: 8 residues within 4Å: Chain C: I.197, V.209, R.211, T.243, N.244, E.245, L.308, Y.564 Ligand excluded by PLIP GOL.68: 5 residues within 4Å: Chain C: S.659, N.660, K.661, D.688, K.691 Ligand excluded by PLIP GOL.69: 6 residues within 4Å: Chain C: N.695, F.702, F.712, Y.726, F.728 Chain D: Q.49 Ligand excluded by PLIP GOL.70: 4 residues within 4Å: Chain C: L.495, P.496, Q.499, R.506 Ligand excluded by PLIP GOL.71: 3 residues within 4Å: Chain C: W.340, Y.344, F.345 Ligand excluded by PLIP GOL.72: 5 residues within 4Å: Chain C: G.455, R.460, R.506, L.509, G.510 Ligand excluded by PLIP GOL.73: 6 residues within 4Å: Chain C: K.645, S.649, Q.651, T.680, K.681 Chain D: D.191 Ligand excluded by PLIP GOL.74: 6 residues within 4Å: Chain C: P.98, S.146, K.147, G.173, E.174, E.175 Ligand excluded by PLIP GOL.75: 6 residues within 4Å: Chain C: I.332, R.333, P.334, E.365, K.411, R.633 Ligand excluded by PLIP GOL.76: 6 residues within 4Å: Chain C: D.191, K.192, D.193, R.267, G.271 Chain D: Y.678 Ligand excluded by PLIP GOL.77: 7 residues within 4Å: Chain C: L.398, G.399, I.470, S.473, K.475, I.476 Ligands: GOL.78 Ligand excluded by PLIP GOL.78: 4 residues within 4Å: Chain C: K.469, D.472, S.473 Ligands: GOL.77 Ligand excluded by PLIP GOL.79: 4 residues within 4Å: Chain C: F.464, E.465, V.468, R.521 Ligand excluded by PLIP GOL.80: 5 residues within 4Å: Chain C: N.662, K.691, A.730, I.731, N.732 Ligand excluded by PLIP GOL.81: 11 residues within 4Å: Chain C: G.32, T.33, L.34, R.73, K.78, Y.80, S.81, E.85, L.106, A.107, L.141 Ligand excluded by PLIP GOL.84: 10 residues within 4Å: Chain B: A.83, G.84, E.85, M.86, D.87, F.88 Chain D: Y.282, S.488, I.490, Y.504 Ligand excluded by PLIP GOL.85: 8 residues within 4Å: Chain C: K.681 Chain D: H.36, L.37, Y.38, F.39, Y.189, V.190, K.192 Ligand excluded by PLIP GOL.86: 9 residues within 4Å: Chain D: V.668, V.669, N.670, D.714, P.715, E.717, K.722, A.723, K.724 Ligand excluded by PLIP GOL.87: 9 residues within 4Å: Chain D: G.385, D.386, K.388, N.426, L.427, E.430, H.431, N.462, Q.466 Ligand excluded by PLIP GOL.88: 7 residues within 4Å: Chain D: K.457, R.460, D.461, F.464, D.513, L.514, K.517 Ligand excluded by PLIP GOL.89: 7 residues within 4Å: Chain D: K.7, D.9, N.12, V.14, H.16, N.45, Y.46 Ligand excluded by PLIP GOL.90: 8 residues within 4Å: Chain D: K.121, G.122, L.123, W.286, E.293, F.294, Q.295, L.509 Ligand excluded by PLIP GOL.91: 5 residues within 4Å: Chain B: P.64, F.105, V.145 Chain D: R.441, K.442 Ligand excluded by PLIP GOL.92: 9 residues within 4Å: Chain B: H.203, A.204, Q.586 Chain C: A.675, Q.676 Chain D: D.56, R.57, G.58 Ligands: IMD.29 Ligand excluded by PLIP GOL.93: 8 residues within 4Å: Chain B: R.96, N.97, P.98, G.100, Y.178, K.285 Chain D: A.497, D.498 Ligand excluded by PLIP GOL.94: 8 residues within 4Å: Chain D: I.197, V.209, R.211, T.243, N.244, E.245, L.308, Y.564 Ligand excluded by PLIP GOL.95: 5 residues within 4Å: Chain D: S.659, N.660, K.661, D.688, K.691 Ligand excluded by PLIP GOL.96: 6 residues within 4Å: Chain C: Q.49 Chain D: N.695, F.702, F.712, Y.726, F.728 Ligand excluded by PLIP GOL.97: 4 residues within 4Å: Chain D: L.495, P.496, Q.499, R.506 Ligand excluded by PLIP GOL.98: 3 residues within 4Å: Chain D: W.340, Y.344, F.345 Ligand excluded by PLIP GOL.99: 5 residues within 4Å: Chain D: G.455, R.460, R.506, L.509, G.510 Ligand excluded by PLIP GOL.100: 6 residues within 4Å: Chain C: D.191 Chain D: K.645, S.649, Q.651, T.680, K.681 Ligand excluded by PLIP GOL.101: 6 residues within 4Å: Chain D: P.98, S.146, K.147, G.173, E.174, E.175 Ligand excluded by PLIP GOL.102: 6 residues within 4Å: Chain D: I.332, R.333, P.334, E.365, K.411, R.633 Ligand excluded by PLIP GOL.103: 6 residues within 4Å: Chain C: Y.678 Chain D: D.191, K.192, D.193, R.267, G.271 Ligand excluded by PLIP GOL.104: 7 residues within 4Å: Chain D: L.398, G.399, I.470, S.473, K.475, I.476 Ligands: GOL.105 Ligand excluded by PLIP GOL.105: 4 residues within 4Å: Chain D: K.469, D.472, S.473 Ligands: GOL.104 Ligand excluded by PLIP GOL.106: 4 residues within 4Å: Chain D: F.464, E.465, V.468, R.521 Ligand excluded by PLIP GOL.107: 5 residues within 4Å: Chain D: N.662, K.691, A.730, I.731, N.732 Ligand excluded by PLIP GOL.108: 11 residues within 4Å: Chain D: G.32, T.33, L.34, R.73, K.78, Y.80, S.81, E.85, L.106, A.107, L.141 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fredslund, F. et al., Crystal Structure of Alpha-Galactosidase from Lactobacillus Acidophilus Ncfm: Insight Into Tetramer Formation and Substrate Binding. J.Mol.Biol. (2011)

Release Date

2011-08-10

Peptides

ALPHA-GALACTOSIDASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

ALPHA-GALACTOSIDASE

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