- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.95 Å
- Oligo State
- homo-dimer
- Ligands
- 1 x BGC- GLC- GLC- GLC- GLC: alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose
- 2 x GLC- GLC- GLC: alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose
GLC-GLC-GLC.2: 8 residues within 4Å:- Chain A: H.858, D.868, K.869, D.871, W.925, G.957, N.959
- Ligands: SO4.38
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:N.857, A:K.869, A:G.957
GLC-GLC-GLC.4: 8 residues within 4Å:- Chain B: H.858, D.868, K.869, D.871, W.925, G.957, N.959
- Ligands: SO4.77
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:H.858, B:D.871, B:N.959, B:N.959
- Water bridges: B:N.857, B:K.869, B:G.957
- 2 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)
GLC-GLC.3: 11 residues within 4Å:- Chain A: D.1142, L.1147, E.1151, R.1159, Y.1161, H.1163, K.1194, N.1195, T.1251, H.1253
- Ligands: NI.14
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:D.1142, A:E.1151, A:R.1159, A:R.1159, A:H.1253
GLC-GLC.5: 10 residues within 4Å:- Chain B: D.1142, L.1147, E.1151, R.1159, Y.1161, H.1163, N.1195, T.1251, H.1253
- Ligands: NI.49
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:D.1142, B:R.1159, B:R.1159, B:H.1253
- 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-AC1.6: 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-AC1.7: 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.8: 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:S.862, A:G.865, A:D.961
CA.9: 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:A.998, A:D.1093, A:D.1093, H2O.28
CA.10: 5 residues within 4Å:- Chain A: D.1116, E.1118, R.1155, Q.1158, D.1255
5 PLIP interactions:5 interactions with chain A- Metal complexes: A:D.1116, A:E.1118, A:R.1155, A:Q.1158, A:D.1255
CA.43: 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.44: 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:A.998, B:D.1093, B:D.1093, H2O.61
CA.45: 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.11: 14 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
- Ligands: BGC-GLC-GLC-GLC-GLC.1
11 PLIP interactions:7 interactions with chain A, 4 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, A:D.473, B:Q.176
- Salt bridges: A:R.456, B:K.338
BGC.46: 14 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
- Ligands: BGC-GLC-GLC-GLC-GLC.1
10 PLIP interactions:4 interactions with chain A, 6 interactions with chain B- Hydrogen bonds: A:D.293, A:K.338, B:R.456, B:D.473, B:H.547
- Water bridges: A:Y.294, B:D.473, B:D.473
- Salt bridges: A:K.338, B:R.456
- 2 x GLC: alpha-D-glucopyranose(Non-covalent)
GLC.12: 5 residues within 4Å:- Chain A: D.990, H.991, W.992, N.1060, N.1124
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:D.990, A:H.991, A:N.1060, A:N.1124, A:N.1124
- Water bridges: A:W.1059
GLC.47: 5 residues within 4Å:- Chain B: D.990, H.991, W.992, N.1060, N.1124
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:H.991, B:N.1060, B:N.1124
- Water bridges: B:W.1059
- 4 x NI: NICKEL (II) ION(Non-covalent)
NI.13: 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.6, H2O.8, H2O.17
NI.14: 4 residues within 4Å:- Chain A: H.1163, D.1165
- Ligands: GLC-GLC.3, MG.22
4 PLIP interactions:2 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:H.1163, A:D.1165, H2O.1, H2O.28
NI.48: 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.37, H2O.45, H2O.49
NI.49: 4 residues within 4Å:- Chain B: H.1163, D.1165
- Ligands: GLC-GLC.5, MG.57
4 PLIP interactions:2 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:H.1163, B:D.1165, H2O.33, H2O.60
- 20 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
MG.15: 4 residues within 4Å:- Chain A: E.265, G.267, E.272
- 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.3, H2O.11, H2O.15
MG.16: 2 residues within 4Å:- Chain A: Q.636, H.660
4 PLIP interactions:1 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:H.660, H2O.1, H2O.12, H2O.28
MG.17: 1 residues within 4Å:- Chain A: V.51
No protein-ligand interaction detected (PLIP)MG.18: 2 residues within 4Å:- Chain A: E.134, D.135
6 PLIP interactions:1 interactions with chain A, 5 Ligand-Water interactions- Metal complexes: A:D.135, H2O.1, H2O.23, H2O.24, H2O.28, H2O.31
MG.19: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.20: 1 residues within 4Å:- Chain A: E.329
No protein-ligand interaction detected (PLIP)MG.21: 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.10, H2O.13, H2O.18, H2O.21, H2O.30
MG.22: 3 residues within 4Å:- Chain A: D.358, D.1165
- Ligands: NI.14
6 PLIP interactions:2 interactions with chain A, 4 Ligand-Water interactions- Metal complexes: A:D.358, A:D.1165, H2O.1, H2O.4, H2O.18, H2O.26
MG.23: 2 residues within 4Å:- Chain A: D.990, H.991
6 PLIP interactions:1 interactions with chain A, 5 Ligand-Water interactions- Metal complexes: A:H.991, H2O.2, H2O.18, H2O.22, H2O.23, H2O.30
MG.24: 1 residues within 4Å:- Chain A: V.1175
No protein-ligand interaction detected (PLIP)MG.50: 4 residues within 4Å:- Chain A: Q.553
- Chain B: E.265, G.267, E.272
5 PLIP interactions:2 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: B:E.265, B:G.267, H2O.13, H2O.33, H2O.44
MG.51: 3 residues within 4Å:- Chain B: S.634, Q.636, H.660
4 PLIP interactions:1 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: B:H.660, H2O.33, H2O.45, H2O.59
MG.52: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.53: 2 residues within 4Å:- Chain B: E.134, D.135
5 PLIP interactions:1 interactions with chain B, 4 Ligand-Water interactions- Metal complexes: B:D.135, H2O.40, H2O.61, H2O.61, H2O.62
MG.54: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.55: 2 residues within 4Å:- Chain B: D.278, E.329
No protein-ligand interaction detected (PLIP)MG.56: 2 residues within 4Å:- Chain B: D.298, T.311
6 PLIP interactions:1 interactions with chain B, 5 Ligand-Water interactions- Metal complexes: B:D.298, H2O.40, H2O.46, H2O.47, H2O.47, H2O.60
MG.57: 3 residues within 4Å:- Chain B: D.358, D.1165
- Ligands: NI.49
5 PLIP interactions:2 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: B:D.358, B:D.1165, H2O.33, H2O.55, H2O.60
MG.58: 2 residues within 4Å:- Chain B: D.990, H.991
6 PLIP interactions:1 interactions with chain B, 5 Ligand-Water interactions- Metal complexes: B:H.991, H2O.34, H2O.37, H2O.54, H2O.58, H2O.63
MG.59: 1 residues within 4Å:- Chain B: D.1245
6 PLIP interactions:1 interactions with chain B, 5 Ligand-Water interactions- Metal complexes: B:D.1245, H2O.36, H2O.37, H2O.52, H2O.58, H2O.63
- 16 x SO4: SULFATE ION(Non-functional Binders)
SO4.25: 4 residues within 4Å:- Chain A: S.29, G.30, D.31, S.32
Ligand excluded by PLIPSO4.26: 4 residues within 4Å:- Chain A: G.25, A.26, T.90, R.108
Ligand excluded by PLIPSO4.27: 2 residues within 4Å:- Chain A: R.151, H.169
Ligand excluded by PLIPSO4.31: 3 residues within 4Å:- Chain A: S.740, R.767, G.825
Ligand excluded by PLIPSO4.34: 2 residues within 4Å:- Chain A: R.843, R.851
Ligand excluded by PLIPSO4.38: 4 residues within 4Å:- Chain A: N.855, N.857, K.869
- Ligands: GLC-GLC-GLC.2
Ligand excluded by PLIPSO4.61: 6 residues within 4Å:- Chain B: T.371, Y.373, G.520, A.521, N.549
- Ligands: BGC-GLC-GLC-GLC-GLC.1
Ligand excluded by PLIPSO4.62: 4 residues within 4Å:- Chain B: S.29, G.30, D.31, S.32
Ligand excluded by PLIPSO4.63: 4 residues within 4Å:- Chain B: T.24, G.25, A.26, R.108
Ligand excluded by PLIPSO4.64: 2 residues within 4Å:- Chain B: R.151, H.169
Ligand excluded by PLIPSO4.68: 4 residues within 4Å:- Chain B: G.766, Y.803, G.804, D.805
Ligand excluded by PLIPSO4.69: 2 residues within 4Å:- Chain B: R.843, R.851
Ligand excluded by PLIPSO4.72: 3 residues within 4Å:- Chain B: T.930, Q.931, T.932
Ligand excluded by PLIPSO4.74: 2 residues within 4Å:- Chain B: N.1181, N.1182
Ligand excluded by PLIPSO4.76: 3 residues within 4Å:- Chain B: A.1183, T.1184, R.1261
Ligand excluded by PLIPSO4.77: 4 residues within 4Å:- Chain B: N.855, N.857, K.869
- Ligands: GLC-GLC-GLC.4
Ligand excluded by PLIP- 16 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
MES.28: 7 residues within 4Å:- Chain A: L.785, D.801, I.802, Y.808, I.835, Y.836, N.882
Ligand excluded by PLIPMES.29: 8 residues within 4Å:- Chain A: T.218, E.219, G.220, R.222, P.365, H.367
- Chain B: Y.423, W.424
Ligand excluded by PLIPMES.30: 5 residues within 4Å:- Chain A: Y.385, Q.386, Q.387
- Chain B: R.222, Y.223
Ligand excluded by PLIPMES.32: 4 residues within 4Å:- Chain A: W.486
- Chain B: G.419, S.420
- Ligands: BGC-GLC-GLC-GLC-GLC.1
Ligand excluded by PLIPMES.33: 7 residues within 4Å:- Chain A: Y.653, S.654, Q.657, I.659, H.660, D.1013, R.1075
Ligand excluded by PLIPMES.35: 12 residues within 4Å:- Chain A: P.884, A.968, P.969, Q.971, A.972, Y.1015, A.1016, P.1017, Y.1022, V.1097, S.1098, A.1099
Ligand excluded by PLIPMES.36: 7 residues within 4Å:- Chain A: F.993, R.1027, N.1060, L.1061, W.1062, V.1176, D.1177
Ligand excluded by PLIPMES.37: 5 residues within 4Å:- Chain A: Q.352, Y.355, N.1195, T.1196, Y.1249
Ligand excluded by PLIPMES.60: 4 residues within 4Å:- Chain B: Y.200, Y.212, G.214, G.215
Ligand excluded by PLIPMES.65: 4 residues within 4Å:- Chain B: Q.352, Y.355, N.1195, Y.1249
Ligand excluded by PLIPMES.66: 5 residues within 4Å:- Chain A: R.222, Y.223
- Chain B: Y.385, Q.386, Q.387
Ligand excluded by PLIPMES.67: 7 residues within 4Å:- Chain B: Y.653, S.654, Q.657, I.659, H.660, D.1013, R.1075
Ligand excluded by PLIPMES.70: 7 residues within 4Å:- Chain B: L.785, D.801, I.802, Y.808, I.835, Y.836, N.882
Ligand excluded by PLIPMES.71: 13 residues within 4Å:- Chain B: P.884, V.885, A.968, P.969, Q.971, A.972, Y.1015, A.1016, P.1017, Y.1022, V.1097, S.1098, A.1099
Ligand excluded by PLIPMES.73: 8 residues within 4Å:- Chain B: F.993, R.1027, N.1060, L.1061, W.1062, V.1176, D.1177
- Ligands: MES.75
Ligand excluded by PLIPMES.75: 8 residues within 4Å:- Chain B: K.995, R.1027, T.1104, E.1108, L.1111, P.1179, R.1261
- Ligands: MES.73
Ligand excluded by PLIP- 8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.39: 7 residues within 4Å:- Chain A: S.196, D.197, Y.213, R.221, Y.223, T.224, K.225
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:D.197, A:T.224, A:T.224, A:K.225
- Water bridges: A:R.221
EDO.40: 5 residues within 4Å:- Chain A: A.583, Y.584, E.587, F.711, T.712
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:E.587, A:T.712
- Water bridges: A:R.586, A:D.620, A:S.710, A:T.712
EDO.41: 5 residues within 4Å:- Chain A: Q.651, T.652, Y.1015, G.1074, R.1075
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:T.652, A:T.652
- Water bridges: A:R.1075
EDO.42: 8 residues within 4Å:- Chain A: F.478, E.482, L.483, N.525, P.526, S.527, L.530, N.1145
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:E.482, A:N.525, A:S.527, A:N.1145
EDO.78: 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.79: 4 residues within 4Å:- Chain B: A.583, Y.584, F.711, T.712
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:T.712
- Water bridges: B:D.620, B:S.710, B:T.712
EDO.80: 5 residues within 4Å:- Chain B: Q.651, T.652, Y.1015, G.1074, R.1075
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:T.652, B:T.652
- Water bridges: B:R.1075
EDO.81: 7 residues within 4Å:- Chain B: F.478, E.482, L.483, N.525, P.526, S.527, L.530
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:E.482, B:N.525, B:S.527, B:N.1145
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- 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
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.95 Å
- Oligo State
- homo-dimer
- Ligands
- 1 x BGC- GLC- GLC- GLC- GLC: alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose
- 2 x GLC- GLC- GLC: alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose
- 2 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)
- 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)
- 6 x CA: CALCIUM ION(Non-covalent)
- 2 x BGC: beta-D-glucopyranose(Non-covalent)
- 2 x GLC: alpha-D-glucopyranose(Non-covalent)
- 4 x NI: NICKEL (II) ION(Non-covalent)
- 20 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 16 x SO4: SULFATE ION(Non-functional Binders)
- 16 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
- 8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- 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
AB
B