- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- homo-dimer
- Ligands
- 7 x GLC- 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-(1-4)-alpha-D-glucopyranose(Non-covalent)
- 1 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)
GLC-AC1.4: 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-AC1.9: 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:K.995, A:A.998, A:D.1093, A:D.1093, H2O.15
CA.13: 6 residues within 4Å:- Chain A: D.1116, E.1118, R.1155, Q.1158, D.1255, E.1256
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.32: 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:S.862, B:G.865, B:D.961
CA.33: 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:K.995, B:A.998, B:D.1093, B:D.1093, H2O.30
CA.34: 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:D.1255
- 2 x NI: NICKEL (II) ION(Non-covalent)
NI.14: 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.3, H2O.6, H2O.9
NI.35: 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.18, H2O.22, H2O.30
- 12 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
MG.15: 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.3, H2O.4, H2O.7
MG.16: 1 residues within 4Å:- Chain A: V.51
No protein-ligand interaction detected (PLIP)MG.17: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.18: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.19: 1 residues within 4Å:- Chain A: E.329
No protein-ligand interaction detected (PLIP)MG.20: 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.8, H2O.11, H2O.11, H2O.12, H2O.15
MG.36: 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.20, H2O.20, H2O.23
MG.37: 1 residues within 4Å:- Chain B: V.51
No protein-ligand interaction detected (PLIP)MG.38: 1 residues within 4Å:- Chain B: E.134
No protein-ligand interaction detected (PLIP)MG.39: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.40: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.41: 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.17, H2O.18, H2O.19, H2O.20, H2O.30
- 12 x SO4: SULFATE ION(Non-functional Binders)
SO4.21: 4 residues within 4Å:- Chain A: G.25, A.26, T.90, R.108
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:A.26, A:A.26
- Salt bridges: A:R.108
SO4.22: 2 residues within 4Å:- Chain A: R.151, H.169
4 PLIP interactions:4 interactions with chain A- Water bridges: A:D.168, A:H.169
- Salt bridges: A:R.151, A:H.169
SO4.23: 3 residues within 4Å:- Chain A: Y.385, Q.386, Q.387
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Q.387
- Water bridges: A:Y.385, A:R.390
SO4.24: 4 residues within 4Å:- Chain A: S.740, R.767, G.825, S.826
3 PLIP interactions:3 interactions with chain A- Water bridges: A:S.740, A:R.767
- Salt bridges: A:R.767
SO4.26: 2 residues within 4Å:- Chain A: R.843, R.851
3 PLIP interactions:3 interactions with chain A- Water bridges: A:R.843
- Salt bridges: A:R.843, A:R.851
SO4.42: 3 residues within 4Å:- Chain B: G.25, A.26, R.108
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:A.26
- Water bridges: B:R.108
- Salt bridges: B:R.108
SO4.43: 2 residues within 4Å:- Chain B: R.151, H.169
3 PLIP interactions:3 interactions with chain B- Water bridges: B:H.169
- Salt bridges: B:R.151, B:H.169
SO4.45: 3 residues within 4Å:- Chain B: Y.385, Q.386, Q.387
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:Q.387
- Water bridges: B:R.390
SO4.47: 2 residues within 4Å:- Chain B: S.740, R.767
1 PLIP interactions:1 interactions with chain B- Salt bridges: B:R.767
SO4.48: 2 residues within 4Å:- Chain B: R.843, R.851
4 PLIP interactions:4 interactions with chain B- Water bridges: B:K.869, B:K.869
- Salt bridges: B:R.843, B:R.851
SO4.51: 3 residues within 4Å:- Chain B: T.930, Q.931, T.932
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:T.932, B:T.932
SO4.53: 2 residues within 4Å:- Chain B: N.1181, N.1182
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:N.1181, B:N.1182
- 7 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
MES.25: 8 residues within 4Å:- Chain A: T.652, Y.653, S.654, Q.657, I.659, H.660, D.1013, R.1075
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:S.654, A:Q.657, A:H.660
- Salt bridges: A:D.1013, A:R.1075
MES.27: 7 residues within 4Å:- Chain A: F.993, R.1027, N.1060, L.1061, W.1062, V.1176, D.1177
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:W.1062, A:D.1177
- Water bridges: A:R.1027, A:R.1027
- Salt bridges: A:R.1027
MES.44: 5 residues within 4Å:- Chain B: Q.352, Y.355, N.1195, T.1196, Y.1249
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:Q.352
- pi-Cation interactions: B:Y.1249
MES.46: 8 residues within 4Å:- Chain B: T.652, Y.653, S.654, Q.657, I.659, H.660, D.1013, R.1075
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:S.654, B:Q.657, B:H.660
- Salt bridges: B:D.1013, B:R.1075
MES.49: 7 residues within 4Å:- Chain B: L.785, D.801, I.802, Y.808, I.835, Y.836, N.882
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:I.802, B:N.882, B:N.882
MES.50: 13 residues within 4Å:- Chain B: P.884, V.885, A.968, P.969, T.970, Q.971, A.972, Y.1015, A.1016, P.1017, V.1097, S.1098, A.1099
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:A.1099
- Water bridges: B:Q.651
MES.52: 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
- 8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.28: 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.29: 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
- Water bridges: A:Y.584, A:E.587, A:T.712
EDO.30: 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, A:R.1075
EDO.31: 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.54: 7 residues within 4Å:- Chain B: S.196, D.197, Y.213, R.221, Y.223, T.224, K.225
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:D.197, B:K.225
EDO.55: 5 residues within 4Å:- Chain B: A.583, E.587, D.620, F.711, T.712
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:E.587, B:T.712
- Water bridges: B:Y.584, B:D.620, B:T.712
EDO.56: 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
- Water bridges: B:R.1075
EDO.57: 7 residues within 4Å:- Chain B: F.478, E.482, L.483, N.525, P.526, S.527, L.530
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:E.482, B:N.525, B:S.527
- 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 2.40 Å
- Oligo State
- homo-dimer
- Ligands
- 7 x GLC- 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-(1-4)-alpha-D-glucopyranose(Non-covalent)
- 1 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 NI: NICKEL (II) ION(Non-covalent)
- 12 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 12 x SO4: SULFATE ION(Non-functional Binders)
- 7 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