SMTL ID : 5x7q.1

Crystal structure of Paenibacillus sp. 598K alpha-1,6-glucosyltransferase complexed with maltohexaose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

1 x GLC- GLC- GLC- GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose

GLC-GLC-GLC-GLC-GLC.1: 9 residues within 4Å: Chain A: M.17, Y.200, Y.202, D.204, K.208, E.210, Y.212, G.214, G.215 No protein-ligand interaction detected (PLIP)

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

GLC-GLC.2: 7 residues within 4Å: Chain A: H.858, D.868, K.869, D.871, W.925, G.957, N.959 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.858, A:D.871, A:N.959, A:N.959 Water bridges: A:D.868, A:K.869, A:G.957 GLC-GLC.6: 7 residues within 4Å: Chain B: H.858, D.868, K.869, D.871, W.925, G.957, N.959 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:H.858, B:D.871, B:N.959, B:N.959 Water bridges: B:N.857, B:N.857, B:K.869, B:W.925, B:G.957

2 x GLC- GLC- GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose

GLC-GLC-GLC-GLC.3: 8 residues within 4Å: Chain A: D.990, H.991, W.992, M.1057, N.1058, W.1059, N.1060, N.1124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.990, A:N.1124 GLC-GLC-GLC-GLC.5: 9 residues within 4Å: Chain B: M.17, Y.200, Y.202, D.204, K.208, E.210, Y.212, G.214, G.215 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.202, B:D.204

2 x BGC- GLC- GLC- GLC: alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose

BGC-GLC-GLC-GLC.4: 19 residues within 4Å: Chain A: R.344, R.350, Y.354, D.358, A.1138, D.1142, L.1147, H.1148, E.1151, R.1159, Y.1161, H.1163, D.1165, K.1194, N.1195, Y.1249, T.1251, H.1253 Ligands: SO4.65 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.358, A:A.1138, A:D.1165, A:D.1165, A:R.350, A:Y.354 Water bridges: A:R.344, A:H.1148 Salt bridges: A:R.344, A:R.350 BGC-GLC-GLC-GLC.8: 19 residues within 4Å: Chain B: R.344, R.350, Y.354, D.358, A.1138, D.1142, L.1147, H.1148, E.1151, R.1159, Y.1161, H.1163, S.1164, D.1165, K.1194, N.1195, T.1251, H.1253 Ligands: SO4.33 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.358, B:A.1138, B:D.1165, B:R.350, B:Y.354 Water bridges: B:R.344, B:R.350 Salt bridges: B:R.344, B:R.350

1 x GLC- GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose

GLC-GLC-GLC.7: 8 residues within 4Å: Chain B: D.990, H.991, W.992, M.1057, N.1058, W.1059, N.1060, N.1124 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.990, B:W.992, B:N.1060, B:N.1124

2 x GLC- AC1: 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-AC1.9: 6 residues within 4Å: Chain A: W.1130, S.1171, H.1173, R.1202, E.1204, Y.1243 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.1171, A:R.1202, A:E.1204, A:E.1204 GLC-AC1.10: 6 residues within 4Å: Chain B: W.1130, S.1171, H.1173, R.1202, E.1204, Y.1243 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.1171, B:R.1202, B:E.1204, B:E.1204

6 x CA: CALCIUM ION(Non-covalent)

CA.11: 5 residues within 4Å: Chain A: E.837, E.839, S.862, G.865, D.961 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.837, A:E.839, A:G.865, A:D.961, A:D.961 CA.12: 4 residues within 4Å: Chain A: E.977, K.995, A.998, D.1093 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.977, A:K.995, A:A.998, A:D.1093, H2O.12 CA.13: 5 residues within 4Å: Chain A: D.1116, E.1118, R.1155, Q.1158, D.1255 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.1116, A:R.1155, A:Q.1158, A:D.1255, H2O.2 CA.39: 5 residues within 4Å: Chain B: E.837, E.839, S.862, G.865, D.961 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.837, B:E.839, B:G.865, B:D.961, B:D.961 CA.40: 4 residues within 4Å: Chain B: E.977, K.995, A.998, D.1093 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.977, B:K.995, B:A.998, B:D.1093, H2O.44 CA.41: 6 residues within 4Å: Chain B: D.1116, E.1118, R.1155, Q.1158, D.1255, E.1256 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.1116, B:E.1118, B:R.1155, B:Q.1158, B:E.1256

2 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.14: 13 residues within 4Å: Chain A: W.409, D.411, E.412, R.456, W.470, D.473, F.515, H.547 Chain B: W.266, D.293, Y.294, I.336, K.338 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.456, A:D.473, A:H.547, B:D.293, B:K.338 Water bridges: A:W.470, A:D.473 Salt bridges: A:R.456, B:K.338 BGC.42: 13 residues within 4Å: Chain A: W.266, D.293, Y.294, I.336, K.338 Chain B: W.409, D.411, E.412, R.456, W.470, D.473, F.515, H.547 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.456, B:D.473, B:H.547, A:D.293, A:K.338 Water bridges: B:D.473, B:D.473 Salt bridges: B:R.456, A:K.338

2 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.15: 7 residues within 4Å: Chain A: H.991, D.1001, N.1002, T.1004, W.1059, N.1089, N.1091 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.991, A:N.1002, A:N.1089, A:N.1091, A:N.1091 Water bridges: A:H.991 GLC.43: 6 residues within 4Å: Chain B: H.991, D.1001, N.1002, W.1059, N.1089, N.1091 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.991, B:N.1002, B:N.1089, B:N.1091, B:N.1091

2 x NI: NICKEL (II) ION(Non-covalent)

NI.16: 3 residues within 4Å: Chain A: H.169, H.172, D.178 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.169, A:H.172, A:D.178, H2O.4, H2O.4, H2O.15 NI.44: 3 residues within 4Å: Chain B: H.169, H.172, D.178 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.169, B:H.172, B:D.178, H2O.35, H2O.37, H2O.45

12 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.17: 3 residues within 4Å: Chain A: E.265, G.267 Chain B: Q.553 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.265, A:G.267, H2O.5, H2O.40, H2O.46 MG.18: 1 residues within 4Å: Chain A: V.51 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Chain A: E.134 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Chain A: N.146 No protein-ligand interaction detected (PLIP) MG.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Chain A: D.298 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.298, H2O.9, H2O.14, H2O.18, H2O.24, H2O.26 MG.45: 3 residues within 4Å: Chain A: Q.553 Chain B: E.265, G.267 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.265, B:G.267, H2O.32, H2O.38, H2O.39 MG.46: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.47: 1 residues within 4Å: Chain B: E.134 No protein-ligand interaction detected (PLIP) MG.48: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.49: 1 residues within 4Å: Chain B: E.329 No protein-ligand interaction detected (PLIP) MG.50: 1 residues within 4Å: Chain B: D.298 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.298, H2O.35, H2O.40, H2O.44, H2O.46, H2O.55

17 x SO4: SULFATE ION(Non-functional Binders)

SO4.23: 5 residues within 4Å: Chain A: T.24, G.25, A.26, T.90, R.108 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain A: R.151, H.169 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain A: L.163, R.164, N.165, S.166, S.167 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain A: Y.385, Q.386, Q.387 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain A: S.740, R.767, G.825 Ligand excluded by PLIP SO4.30: 2 residues within 4Å: Chain A: R.843, R.851 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain A: R.380 Ligands: BGC-GLC-GLC-GLC.8 Ligand excluded by PLIP SO4.51: 5 residues within 4Å: Chain B: T.24, G.25, A.26, T.90, R.108 Ligand excluded by PLIP SO4.52: 2 residues within 4Å: Chain B: R.151, H.169 Ligand excluded by PLIP SO4.54: 3 residues within 4Å: Chain B: Y.385, Q.386, Q.387 Ligand excluded by PLIP SO4.56: 3 residues within 4Å: Chain B: S.740, R.767, G.825 Ligand excluded by PLIP SO4.57: 2 residues within 4Å: Chain B: R.843, R.851 Ligand excluded by PLIP SO4.60: 4 residues within 4Å: Chain B: H.858, A.924, W.925, S.926 Ligand excluded by PLIP SO4.61: 3 residues within 4Å: Chain B: T.930, Q.931, T.932 Ligand excluded by PLIP SO4.63: 2 residues within 4Å: Chain B: N.1181, N.1182 Ligand excluded by PLIP SO4.64: 4 residues within 4Å: Chain B: A.1183, T.1184, R.1261, A.1262 Ligand excluded by PLIP SO4.65: 3 residues within 4Å: Chain A: D.358 Chain B: R.380 Ligands: BGC-GLC-GLC-GLC.4 Ligand excluded by PLIP

9 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.26: 8 residues within 4Å: Chain A: T.218, E.219, G.220, R.222, P.365, H.367 Chain B: Y.423, W.424 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.221, B:W.424 MES.29: 7 residues within 4Å: Chain A: Y.653, S.654, Q.657, I.659, H.660, D.1013, R.1075 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.654, A:Q.657, A:H.660 Salt bridges: A:R.1075 MES.31: 10 residues within 4Å: Chain A: P.884, P.969, A.972, Y.1015, A.1016, P.1017, Y.1022, V.1097, S.1098, A.1099 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.1099 Water bridges: A:G.1074 MES.32: 7 residues within 4Å: Chain A: F.993, R.1027, N.1060, L.1061, W.1062, V.1176, D.1177 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.1062, A:D.1177 Salt bridges: A:R.1027 MES.53: 5 residues within 4Å: Chain B: Q.352, Y.355, N.1195, T.1196, Y.1249 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.352, B:T.1196 pi-Cation interactions: B:Y.355 MES.55: 7 residues within 4Å: Chain B: Y.653, S.654, Q.657, I.659, H.660, D.1013, R.1075 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.654, B:Q.657, B:H.660 Salt bridges: B:R.1075 MES.58: 7 residues within 4Å: Chain B: L.785, D.801, I.802, Y.808, I.835, Y.836, N.882 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.802, B:N.882 Water bridges: B:I.835, B:Y.836, B:N.882 MES.59: 12 residues within 4Å: Chain B: P.884, V.885, A.968, P.969, A.972, Y.1015, A.1016, P.1017, Y.1022, V.1097, S.1098, A.1099 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.1099 MES.62: 7 residues within 4Å: Chain B: F.993, R.1027, N.1060, L.1061, W.1062, V.1176, D.1177 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.1062, B:D.1177 Salt bridges: B:R.1027

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

EDO.34: 7 residues within 4Å: Chain A: S.196, D.197, Y.213, R.221, Y.223, T.224, K.225 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.197, A:K.225 Water bridges: A:K.225 EDO.35: 5 residues within 4Å: Chain A: A.583, Y.584, E.587, F.711, T.712 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.587, A:T.712, A:T.712 Water bridges: A:E.587, A:D.620 EDO.36: 4 residues within 4Å: Chain A: Q.651, T.652, Y.1015, R.1075 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.652, A:T.652 Water bridges: A:R.1075 EDO.37: 6 residues within 4Å: Chain A: F.478, E.482, L.483, P.526, S.527, L.530 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.482, A:S.527, A:N.1145 EDO.38: 7 residues within 4Å: Chain A: E.1064, R.1094, I.1102, T.1103, T.1104, L.1105, E.1108 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.1094, A:L.1105 Water bridges: A:S.1025, A:S.1025 EDO.66: 7 residues within 4Å: Chain B: S.196, D.197, Y.213, R.221, Y.223, T.224, K.225 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.197, B:K.225 Water bridges: B:R.221, B:K.225 EDO.67: 4 residues within 4Å: Chain B: A.583, Y.584, F.711, T.712 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.587, B:E.587, B:T.712 Water bridges: B:E.587, B:D.620, B:S.710, B:T.712 EDO.68: 5 residues within 4Å: Chain B: Q.651, T.652, Y.1015, G.1074, R.1075 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.652, B:T.652 EDO.69: 7 residues within 4Å: Chain B: F.478, E.482, L.483, P.526, S.527, L.530, N.1145 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.482, B:N.525, B:S.527, B:N.1145 EDO.70: 7 residues within 4Å: Chain B: E.1064, R.1094, I.1102, T.1103, T.1104, L.1105, E.1108 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.1094, B:L.1105 Water bridges: B:S.1025, B:S.1025

Links

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Citation

Fujimoto, Z. et al., Carbohydrate-binding architecture of the multi-modular alpha-1,6-glucosyltransferase from Paenibacillus sp. 598K, which produces alpha-1,6-glucosyl-alpha-glucosaccharides from starch. Biochem. J. (2017)

Release Date

2017-07-26

Peptides

Glycoside hydrolase family 31 alpha-glucosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycoside hydrolase family 31 alpha-glucosidase

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