SMTL ID : 8iuc.1

Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae in complex with isomaltose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-hexamer

Ligands

6 x BGC- GLC: alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose(Non-covalent)

BGC-GLC.1: 17 residues within 4Å: Chain C: R.71, Y.334, F.339, W.388, E.389, T.398, P.399, A.402, L.403, T.404, V.465, E.469, W.470, E.472, K.535 Ligands: EDO.25, EDO.26 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:L.403, C:W.470, C:E.472, C:R.71, C:R.71, C:Y.334, C:W.388, C:E.469, C:K.535 Water bridges: C:K.535 Salt bridges: C:K.535 BGC-GLC.2: 17 residues within 4Å: Chain A: R.71, Y.334, F.339, W.388, E.389, T.398, P.399, A.402, L.403, T.404, V.465, E.469, W.470, E.472, K.535 Ligands: EDO.5, EDO.6 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:L.403, A:T.404, A:W.470, A:E.472, A:R.71, A:R.71, A:W.388, A:E.389, A:T.404, A:E.469, A:K.535 Water bridges: A:K.535, A:K.535, A:H.337 Salt bridges: A:K.535 BGC-GLC.3: 17 residues within 4Å: Chain B: R.71, Y.334, F.339, W.388, E.389, T.398, P.399, A.402, L.403, T.404, V.465, E.469, W.470, E.472, K.535 Ligands: EDO.14, EDO.16 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:L.403, B:W.470, B:R.71, B:Y.334, B:W.388, B:E.389, B:T.404, B:E.469, B:K.535 Salt bridges: B:K.535 Water bridges: B:R.71 BGC-GLC.34: 17 residues within 4Å: Chain F: R.71, Y.334, F.339, W.388, E.389, T.398, P.399, A.402, L.403, T.404, V.465, E.469, W.470, E.472, K.535 Ligands: EDO.58, EDO.59 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:L.403, F:W.470, F:R.71, F:R.71, F:Y.334, F:W.388, F:E.389, F:E.469, F:K.535 Water bridges: F:K.535 Salt bridges: F:K.535 BGC-GLC.35: 17 residues within 4Å: Chain D: R.71, Y.334, F.339, W.388, E.389, T.398, P.399, A.402, L.403, T.404, V.465, E.469, W.470, E.472, K.535 Ligands: EDO.38, EDO.39 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:L.403, D:T.404, D:W.470, D:R.71, D:R.71, D:W.388, D:T.404, D:E.469, D:K.535 Water bridges: D:K.535, D:K.535, D:H.337 Salt bridges: D:K.535 BGC-GLC.36: 17 residues within 4Å: Chain E: R.71, Y.334, F.339, W.388, E.389, T.398, P.399, A.402, L.403, T.404, V.465, E.469, W.470, E.472, K.535 Ligands: EDO.47, EDO.49 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:L.403, E:W.470, E:E.472, E:R.71, E:Y.334, E:W.388, E:T.404, E:E.469, E:K.535 Salt bridges: E:K.535 Water bridges: E:R.71

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

EDO.4: 7 residues within 4Å: Chain A: R.71, M.327, G.333, Y.334, N.335, E.613, N.619 Ligand excluded by PLIP EDO.5: 10 residues within 4Å: Chain A: P.326, Y.334, F.339, D.341, W.388, E.469, M.574, E.613, F.622 Ligands: BGC-GLC.2 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: R.71, G.72, P.399, N.401, A.402 Chain E: N.222 Ligands: BGC-GLC.2, BGC-GLC.2 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: V.143, L.206, F.207, D.208, S.242, F.243, A.244, K.274 Ligand excluded by PLIP EDO.8: 11 residues within 4Å: Chain A: D.304, S.307, M.308, H.311, Y.600, L.604, F.608, R.609, V.610, I.611, Y.621 Ligand excluded by PLIP EDO.9: 9 residues within 4Å: Chain A: H.20, Q.21, L.26, S.27, Q.300, Q.303, P.607, F.608, R.609 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: P.215, E.216, I.217, L.218, S.230, F.231, D.232 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: D.22, P.23, W.24, K.25, R.110 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: W.24, R.110, N.286, W.289 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: K.429, V.497, L.498, G.499 Ligand excluded by PLIP EDO.14: 10 residues within 4Å: Chain B: P.326, Y.334, F.339, D.341, W.388, E.469, M.574, E.613, F.622 Ligands: BGC-GLC.3 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain B: R.71, M.327, G.333, Y.334, N.335, E.613, N.619 Ligand excluded by PLIP EDO.16: 8 residues within 4Å: Chain B: R.71, G.72, P.399, N.401, A.402 Chain D: N.222 Ligands: BGC-GLC.3, BGC-GLC.3 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: Q.650, T.673, F.674, V.675, L.676 Ligand excluded by PLIP EDO.18: 8 residues within 4Å: Chain B: V.143, L.206, F.207, D.208, S.242, F.243, A.244, K.274 Ligand excluded by PLIP EDO.19: 11 residues within 4Å: Chain B: D.304, S.307, M.308, H.311, Y.600, L.604, F.608, R.609, V.610, I.611, Y.621 Ligand excluded by PLIP EDO.20: 9 residues within 4Å: Chain B: H.20, K.25, L.26, S.27, Q.300, Q.303, P.607, F.608, R.609 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: D.22, P.23, W.24, K.25, R.110 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: Q.170, Y.172, V.189, K.198, Y.259 Chain E: Q.170 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain B: F.191, G.195, R.196, S.197, K.198, S.252 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain C: R.71, M.327, G.333, Y.334, E.613, N.619 Ligand excluded by PLIP EDO.25: 10 residues within 4Å: Chain C: P.326, Y.334, F.339, D.341, W.388, E.469, M.574, E.613, F.622 Ligands: BGC-GLC.1 Ligand excluded by PLIP EDO.26: 9 residues within 4Å: Chain C: R.71, G.72, P.399, N.401, A.402 Chain F: N.222, D.223 Ligands: BGC-GLC.1, BGC-GLC.1 Ligand excluded by PLIP EDO.27: 8 residues within 4Å: Chain C: V.143, L.206, F.207, D.208, S.242, F.243, A.244, K.274 Ligand excluded by PLIP EDO.28: 11 residues within 4Å: Chain C: D.304, S.307, M.308, H.311, Y.600, L.604, F.608, R.609, V.610, I.611, Y.621 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain C: H.20, L.26, S.27, Q.300, Q.303, P.607, F.608, R.609 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain C: D.22, P.23, W.24, K.25, R.110 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain C: N.168, F.191, G.195 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain C: Q.367, R.368, D.392, S.393 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain C: F.191, G.195, R.196, S.197, K.198, S.252 Ligand excluded by PLIP EDO.37: 7 residues within 4Å: Chain D: R.71, M.327, G.333, Y.334, N.335, E.613, N.619 Ligand excluded by PLIP EDO.38: 10 residues within 4Å: Chain D: P.326, Y.334, F.339, D.341, W.388, E.469, M.574, E.613, F.622 Ligands: BGC-GLC.35 Ligand excluded by PLIP EDO.39: 8 residues within 4Å: Chain B: N.222 Chain D: R.71, G.72, P.399, N.401, A.402 Ligands: BGC-GLC.35, BGC-GLC.35 Ligand excluded by PLIP EDO.40: 8 residues within 4Å: Chain D: V.143, L.206, F.207, D.208, S.242, F.243, A.244, K.274 Ligand excluded by PLIP EDO.41: 11 residues within 4Å: Chain D: D.304, S.307, M.308, H.311, Y.600, L.604, F.608, R.609, V.610, I.611, Y.621 Ligand excluded by PLIP EDO.42: 9 residues within 4Å: Chain D: H.20, Q.21, L.26, S.27, Q.300, Q.303, P.607, F.608, R.609 Ligand excluded by PLIP EDO.43: 7 residues within 4Å: Chain D: P.215, E.216, I.217, L.218, S.230, F.231, D.232 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain D: D.22, P.23, W.24, K.25, R.110 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain D: W.24, R.110, N.286, W.289 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain D: K.429, V.497, L.498, G.499 Ligand excluded by PLIP EDO.47: 10 residues within 4Å: Chain E: P.326, Y.334, F.339, D.341, W.388, E.469, M.574, E.613, F.622 Ligands: BGC-GLC.36 Ligand excluded by PLIP EDO.48: 7 residues within 4Å: Chain E: R.71, M.327, G.333, Y.334, N.335, E.613, N.619 Ligand excluded by PLIP EDO.49: 8 residues within 4Å: Chain A: N.222 Chain E: R.71, G.72, P.399, N.401, A.402 Ligands: BGC-GLC.36, BGC-GLC.36 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain E: Q.650, T.673, F.674, V.675, L.676 Ligand excluded by PLIP EDO.51: 8 residues within 4Å: Chain E: V.143, L.206, F.207, D.208, S.242, F.243, A.244, K.274 Ligand excluded by PLIP EDO.52: 11 residues within 4Å: Chain E: D.304, S.307, M.308, H.311, Y.600, L.604, F.608, R.609, V.610, I.611, Y.621 Ligand excluded by PLIP EDO.53: 9 residues within 4Å: Chain E: H.20, K.25, L.26, S.27, Q.300, Q.303, P.607, F.608, R.609 Ligand excluded by PLIP EDO.54: 5 residues within 4Å: Chain E: D.22, P.23, W.24, K.25, R.110 Ligand excluded by PLIP EDO.55: 6 residues within 4Å: Chain B: Q.170 Chain E: Q.170, Y.172, V.189, K.198, Y.259 Ligand excluded by PLIP EDO.56: 6 residues within 4Å: Chain E: F.191, G.195, R.196, S.197, K.198, S.252 Ligand excluded by PLIP EDO.57: 6 residues within 4Å: Chain F: R.71, M.327, G.333, Y.334, E.613, N.619 Ligand excluded by PLIP EDO.58: 10 residues within 4Å: Chain F: P.326, Y.334, F.339, D.341, W.388, E.469, M.574, E.613, F.622 Ligands: BGC-GLC.34 Ligand excluded by PLIP EDO.59: 9 residues within 4Å: Chain C: N.222, D.223 Chain F: R.71, G.72, P.399, N.401, A.402 Ligands: BGC-GLC.34, BGC-GLC.34 Ligand excluded by PLIP EDO.60: 8 residues within 4Å: Chain F: V.143, L.206, F.207, D.208, S.242, F.243, A.244, K.274 Ligand excluded by PLIP EDO.61: 11 residues within 4Å: Chain F: D.304, S.307, M.308, H.311, Y.600, L.604, F.608, R.609, V.610, I.611, Y.621 Ligand excluded by PLIP EDO.62: 8 residues within 4Å: Chain F: H.20, L.26, S.27, Q.300, Q.303, P.607, F.608, R.609 Ligand excluded by PLIP EDO.63: 5 residues within 4Å: Chain F: D.22, P.23, W.24, K.25, R.110 Ligand excluded by PLIP EDO.64: 3 residues within 4Å: Chain F: N.168, F.191, G.195 Ligand excluded by PLIP EDO.65: 4 residues within 4Å: Chain F: Q.367, R.368, D.392, S.393 Ligand excluded by PLIP EDO.66: 6 residues within 4Å: Chain F: F.191, G.195, R.196, S.197, K.198, S.252 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, S. et al., Bacteroidota polysaccharide utilization system for branched dextran exopolysaccharides from lactic acid bacteria. J.Biol.Chem. (2023)

Release Date

2023-06-14

Peptides

Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65

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