SMTL ID : 2xn0.1

Structure of alpha-galactosidase from Lactobacillus acidophilus NCFM, PtCl4 derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

34 x PT: PLATINUM (II) ION(Non-covalent)(Non-functional Binders)

PT.1: 3 residues within 4Å: Chain A: M.672, H.674 Chain C: K.561 Ligand excluded by PLIP PT.2: 3 residues within 4Å: Chain A: H.709 Ligands: PT.3, PT.5 Ligand excluded by PLIP PT.3: 3 residues within 4Å: Chain A: H.709 Ligands: PT.2, PT.5 Ligand excluded by PLIP PT.4: 2 residues within 4Å: Chain A: M.708 Ligands: PT.5 Ligand excluded by PLIP PT.5: 5 residues within 4Å: Chain A: M.708, H.709 Ligands: PT.2, PT.3, PT.4 Ligand excluded by PLIP PT.6: 2 residues within 4Å: Chain A: M.247 Chain D: G.248 Ligand excluded by PLIP PT.7: 2 residues within 4Å: Chain A: M.601, M.725 Ligand excluded by PLIP PT.8: 3 residues within 4Å: Chain A: M.672 Chain C: M.672 Ligands: PT.38 Ligand excluded by PLIP PT.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PT.17: 3 residues within 4Å: Chain B: M.672 Chain D: M.672 Ligands: PT.47 Ligand excluded by PLIP PT.18: 1 residues within 4Å: Chain B: H.674 Ligand excluded by PLIP PT.19: 3 residues within 4Å: Chain B: H.709 Ligands: PT.20, PT.22 Ligand excluded by PLIP PT.20: 3 residues within 4Å: Chain B: H.709 Ligands: PT.19, PT.22 Ligand excluded by PLIP PT.21: 2 residues within 4Å: Chain B: M.708 Ligands: PT.22 Ligand excluded by PLIP PT.22: 5 residues within 4Å: Chain B: M.708, H.709 Ligands: PT.19, PT.20, PT.21 Ligand excluded by PLIP PT.23: 2 residues within 4Å: Chain B: M.247 Chain C: G.248 Ligand excluded by PLIP PT.24: 1 residues within 4Å: Chain B: M.725 Ligand excluded by PLIP PT.31: 3 residues within 4Å: Chain A: K.561 Chain C: M.672, H.674 Ligand excluded by PLIP PT.32: 3 residues within 4Å: Chain C: H.709 Ligands: PT.33, PT.35 Ligand excluded by PLIP PT.33: 3 residues within 4Å: Chain C: H.709 Ligands: PT.32, PT.35 Ligand excluded by PLIP PT.34: 2 residues within 4Å: Chain C: M.708 Ligands: PT.35 Ligand excluded by PLIP PT.35: 5 residues within 4Å: Chain C: M.708, H.709 Ligands: PT.32, PT.33, PT.34 Ligand excluded by PLIP PT.36: 2 residues within 4Å: Chain B: G.248 Chain C: M.247 Ligand excluded by PLIP PT.37: 2 residues within 4Å: Chain C: M.601, M.725 Ligand excluded by PLIP PT.38: 3 residues within 4Å: Chain A: M.672 Chain C: M.672 Ligands: PT.8 Ligand excluded by PLIP PT.46: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PT.47: 3 residues within 4Å: Chain B: M.672 Chain D: M.672 Ligands: PT.17 Ligand excluded by PLIP PT.48: 1 residues within 4Å: Chain D: H.674 Ligand excluded by PLIP PT.49: 3 residues within 4Å: Chain D: H.709 Ligands: PT.50, PT.52 Ligand excluded by PLIP PT.50: 3 residues within 4Å: Chain D: H.709 Ligands: PT.49, PT.52 Ligand excluded by PLIP PT.51: 2 residues within 4Å: Chain D: M.708 Ligands: PT.52 Ligand excluded by PLIP PT.52: 5 residues within 4Å: Chain D: M.708, H.709 Ligands: PT.49, PT.50, PT.51 Ligand excluded by PLIP PT.53: 2 residues within 4Å: Chain A: G.248 Chain D: M.247 Ligand excluded by PLIP PT.54: 1 residues within 4Å: Chain D: M.725 Ligand excluded by PLIP

26 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 11 residues within 4Å: Chain A: W.340, D.370, W.415, K.480, D.482, N.484, C.530, G.532, G.533, D.552 Ligands: GOL.12 Ligand excluded by PLIP GOL.10: 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.11: 11 residues within 4Å: Chain A: A.83, G.84, E.85, M.86, D.87, F.88 Chain B: Y.224, Y.282, L.487, S.488, Y.504 Ligand excluded by PLIP GOL.12: 9 residues within 4Å: Chain A: H.203, R.447, N.484, G.532, D.552 Chain B: G.58, F.59 Ligands: GOL.9, GOL.14 Ligand excluded by PLIP GOL.13: 8 residues within 4Å: Chain A: H.316, S.317, H.320, E.321, P.571, Q.572, F.638, G.639 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain A: H.203 Chain B: D.56, G.58 Chain C: A.675, Q.676, R.718 Ligands: GOL.12 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain A: R.325, S.326, V.519, T.520 Ligand excluded by PLIP GOL.25: 11 residues within 4Å: Chain B: W.340, D.370, W.415, K.480, D.482, N.484, C.530, G.533, W.549, D.552 Ligands: GOL.28 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain B: P.98, S.146, K.147, G.173, E.174, E.175 Ligand excluded by PLIP GOL.27: 11 residues within 4Å: Chain A: Y.224, Y.282, L.487, S.488, Y.504 Chain B: A.83, G.84, E.85, M.86, D.87, F.88 Ligand excluded by PLIP GOL.28: 8 residues within 4Å: Chain A: G.58, F.59 Chain B: H.203, R.447, N.484, G.532, D.552 Ligands: GOL.25 Ligand excluded by PLIP GOL.29: 7 residues within 4Å: Chain B: H.316, H.320, E.321, P.571, Q.572, F.638, G.639 Ligand excluded by PLIP GOL.30: 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.39: 11 residues within 4Å: Chain C: W.340, D.370, W.415, K.480, D.482, N.484, C.530, G.532, G.533, D.552 Ligands: GOL.42 Ligand excluded by PLIP GOL.40: 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.41: 11 residues within 4Å: Chain C: A.83, G.84, E.85, M.86, D.87, F.88 Chain D: Y.224, Y.282, L.487, S.488, Y.504 Ligand excluded by PLIP GOL.42: 9 residues within 4Å: Chain C: H.203, R.447, N.484, G.532, D.552 Chain D: G.58, F.59 Ligands: GOL.39, GOL.44 Ligand excluded by PLIP GOL.43: 8 residues within 4Å: Chain C: H.316, S.317, H.320, E.321, P.571, Q.572, F.638, G.639 Ligand excluded by PLIP GOL.44: 7 residues within 4Å: Chain A: A.675, Q.676, R.718 Chain C: H.203 Chain D: D.56, G.58 Ligands: GOL.42 Ligand excluded by PLIP GOL.45: 4 residues within 4Å: Chain C: R.325, S.326, V.519, T.520 Ligand excluded by PLIP GOL.55: 11 residues within 4Å: Chain D: W.340, D.370, W.415, K.480, D.482, N.484, C.530, G.533, W.549, D.552 Ligands: GOL.58 Ligand excluded by PLIP GOL.56: 6 residues within 4Å: Chain D: P.98, S.146, K.147, G.173, E.174, E.175 Ligand excluded by PLIP GOL.57: 11 residues within 4Å: Chain C: Y.224, Y.282, L.487, S.488, Y.504 Chain D: A.83, G.84, E.85, M.86, D.87, F.88 Ligand excluded by PLIP GOL.58: 8 residues within 4Å: Chain C: G.58, F.59 Chain D: H.203, R.447, N.484, G.532, D.552 Ligands: GOL.55 Ligand excluded by PLIP GOL.59: 7 residues within 4Å: Chain D: H.316, H.320, E.321, P.571, Q.572, F.638, G.639 Ligand excluded by PLIP GOL.60: 7 residues within 4Å: Chain D: K.457, R.460, D.461, F.464, D.513, L.514, K.517 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
A

D
B

ALPHA-GALACTOSIDASE

Related Entries With Identical Sequence