SMTL ID : 2xn1.1

Structure of alpha-galactosidase from Lactobacillus acidophilus NCFM with TRIS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 15 residues within 4Å: Chain A: H.203, W.340, D.370, D.371, W.415, R.447, K.480, D.482, N.484, C.530, G.532, G.533, W.549, D.552 Ligands: GOL.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.370, A:W.415, A:K.480, A:D.482, A:N.484, A:G.532, A:G.533 Water bridges: A:R.447 TRS.7: 15 residues within 4Å: Chain B: H.203, W.340, D.370, D.371, W.415, R.447, K.480, D.482, N.484, C.530, G.532, G.533, W.549, D.552 Ligands: GOL.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.370, B:W.415, B:K.480, B:D.482, B:D.482, B:N.484, B:G.533 Water bridges: B:R.447 TRS.15: 14 residues within 4Å: Chain C: H.203, W.340, D.370, W.415, R.447, K.480, D.482, N.484, C.530, G.532, G.533, W.549, D.552 Ligands: GOL.16 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:D.370, C:W.415, C:K.480, C:D.482, C:D.482, C:N.484, C:G.532, C:G.533 Water bridges: C:R.447, C:D.552, C:D.552 TRS.21: 13 residues within 4Å: Chain D: W.340, D.370, W.415, R.447, K.480, D.482, N.484, C.530, G.532, G.533, W.549, D.552 Ligands: GOL.22 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:D.370, D:W.415, D:K.480, D:D.482, D:N.484, D:G.532, D:G.533 Water bridges: D:R.447, D:D.552

21 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: H.203, R.447, N.484, G.532, D.552 Chain B: G.58, F.59 Ligands: TRS.1 Ligand excluded by PLIP GOL.3: 7 residues within 4Å: Chain A: P.98, V.145, S.146, K.147, G.173, E.174, E.175 Ligand excluded by PLIP GOL.4: 14 residues within 4Å: Chain A: G.32, T.33, L.34, R.73, K.78, E.79, Y.80, S.81, S.82, E.85, L.106, A.107, Y.108, L.141 Ligand excluded by PLIP GOL.5: 8 residues within 4Å: Chain A: N.695, T.698, F.702, L.707, F.712, Y.726, F.728 Chain D: Q.49 Ligand excluded by PLIP GOL.6: 13 residues within 4Å: Chain A: A.83, G.84, E.85, M.86, D.87, F.88, N.102 Chain B: Y.224, Y.282, L.487, S.488, I.490, Y.504 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: G.58, F.59 Chain B: H.203, R.447, N.484, G.532 Ligands: TRS.7 Ligand excluded by PLIP GOL.9: 8 residues within 4Å: Chain B: N.695, T.698, F.702, L.707, F.712, Y.726, F.728 Chain C: Q.49 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain B: P.98, V.145, S.146, K.147, G.173, E.174, E.175 Ligand excluded by PLIP GOL.11: 7 residues within 4Å: Chain B: Q.331, I.332, R.333, P.334, E.365, K.411, R.633 Ligand excluded by PLIP GOL.12: 10 residues within 4Å: Chain B: A.673, H.674, A.675, P.677, I.716, E.717, R.718 Chain C: L.55 Chain D: Q.586, N.587 Ligand excluded by PLIP GOL.13: 13 residues within 4Å: Chain A: Y.224, Y.282, L.487, S.488, I.490, Y.504 Chain B: A.83, G.84, E.85, M.86, D.87, F.88, N.102 Ligand excluded by PLIP GOL.14: 14 residues within 4Å: Chain B: G.32, T.33, L.34, R.73, K.78, E.79, Y.80, S.81, S.82, E.85, L.106, A.107, Y.108, L.141 Ligand excluded by PLIP GOL.16: 8 residues within 4Å: Chain C: H.203, R.447, N.484, G.532, D.552 Chain D: G.58, F.59 Ligands: TRS.15 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain C: P.98, V.145, S.146, K.147, G.173, E.174, E.175 Ligand excluded by PLIP GOL.18: 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.19: 13 residues within 4Å: Chain C: A.83, G.84, E.85, M.86, D.87, F.88, N.102 Chain D: Y.224, Y.282, L.487, S.488, I.490, Y.504 Ligand excluded by PLIP GOL.20: 13 residues within 4Å: Chain C: G.32, T.33, L.34, R.73, K.78, E.79, Y.80, S.81, S.82, E.85, L.106, A.107, L.141 Ligand excluded by PLIP GOL.22: 7 residues within 4Å: Chain C: G.58, F.59 Chain D: H.203, R.447, N.484, G.532 Ligands: TRS.21 Ligand excluded by PLIP GOL.23: 13 residues within 4Å: Chain C: Y.224, Y.282, L.487, S.488, I.490, Y.504 Chain D: A.83, G.84, E.85, M.86, D.87, F.88, N.102 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain D: P.98, V.145, S.146, K.147, G.173, E.174, E.175 Ligand excluded by PLIP GOL.25: 13 residues within 4Å: Chain D: G.32, T.33, L.34, R.73, K.78, Y.80, S.81, S.82, E.85, L.106, A.107, Y.108, 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
B

C
C

D
D

ALPHA-GALACTOSIDASE

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