SMTL ID : 5x7o.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 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.2: 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.18 CA.3: 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.30: 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.31: 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.59 CA.32: 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 NI: NICKEL (II) ION(Non-covalent)

NI.4: 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.1, H2O.8, H2O.14 NI.33: 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.39, H2O.45, H2O.57

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

MG.5: 4 residues within 4Å: Chain A: E.265, G.267, E.272 Chain B: Q.553 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.265, A:G.267, A:E.272, H2O.52, H2O.59 MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain A: E.134 No protein-ligand interaction detected (PLIP) MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 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.12, H2O.16, H2O.18, H2O.23, H2O.33 MG.11: 2 residues within 4Å: Chain A: D.1116, R.1155 No protein-ligand interaction detected (PLIP) MG.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.28: 4 residues within 4Å: Chain A: Q.553 Chain B: E.265, G.267, E.272 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.265, B:G.267, B:E.272, H2O.20, H2O.56 MG.29: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.34: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.35: 1 residues within 4Å: Chain B: E.134 No protein-ligand interaction detected (PLIP) MG.36: 1 residues within 4Å: Chain B: E.329 No protein-ligand interaction detected (PLIP) MG.37: 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.43, H2O.52, H2O.57, H2O.63, H2O.71 MG.38: 1 residues within 4Å: Chain B: D.951 No protein-ligand interaction detected (PLIP)

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

SO4.12: 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 SO4.13: 2 residues within 4Å: Chain A: R.151, H.169 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.168, A:D.168 Water bridges: A:H.169 Salt bridges: A:R.151, A:H.169 SO4.14: 3 residues within 4Å: Chain A: Y.385, Q.386, Q.387 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.387 Water bridges: A:Y.385, A:A.388, A:R.390 SO4.15: 4 residues within 4Å: Chain A: S.740, R.767, G.825, S.826 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.825 Water bridges: A:R.767 Salt bridges: A:R.767 SO4.16: 2 residues within 4Å: Chain A: R.843, R.851 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.869 Salt bridges: A:R.843, A:R.851 SO4.17: 4 residues within 4Å: Chain A: H.858, A.924, W.925, S.926 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.925, A:S.926 Water bridges: A:H.858 Salt bridges: A:H.858 SO4.39: 5 residues within 4Å: Chain B: T.24, G.25, A.26, T.90, R.108 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.24, B:A.26, B:T.90 Salt bridges: B:R.108 SO4.40: 2 residues within 4Å: Chain B: R.151, H.169 4 PLIP interactions: 4 interactions with chain B Water bridges: B:D.168, B:D.168 Salt bridges: B:R.151, B:H.169 SO4.42: 2 residues within 4Å: Chain A: D.358 Chain B: R.380 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.380 SO4.43: 3 residues within 4Å: Chain B: Y.385, Q.386, Q.387 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.385, B:Q.387 Water bridges: B:A.388, B:R.390 SO4.44: 5 residues within 4Å: Chain B: T.652, Y.653, S.654, Q.657, R.1075 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.654, B:Q.657 Salt bridges: B:R.1075 SO4.45: 2 residues within 4Å: Chain B: R.843, R.851 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.843, B:K.869 Salt bridges: B:R.843, B:R.851 SO4.46: 3 residues within 4Å: Chain B: A.924, W.925, S.926 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.925, B:S.926, B:S.926 Water bridges: B:H.858 SO4.48: 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 SO4.49: 3 residues within 4Å: Chain B: A.1183, T.1184, R.1261 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.1184, B:T.1184 Water bridges: B:N.1232 Salt bridges: B:R.1261

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

MES.18: 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:W.1062 Salt bridges: A:R.1027 MES.19: 6 residues within 4Å: Chain A: Q.352, Y.355, D.356, N.1195, T.1196, Y.1249 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.352, A:Y.1249 pi-Cation interactions: A:Y.1249 MES.41: 4 residues within 4Å: Chain B: Q.352, Y.355, N.1195, Y.1249 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.352, B:Q.352 pi-Cation interactions: B:Y.1249 MES.47: 7 residues within 4Å: Chain B: F.993, R.1027, N.1060, L.1061, W.1062, V.1176, D.1177 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.1062, B:D.1177 Water bridges: B:R.1027 Salt bridges: B:R.1027

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

EDO.20: 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:K.225 Water bridges: A:T.224, A:K.225 EDO.21: 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:S.710, A:T.712 EDO.22: 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.23: 7 residues within 4Å: Chain A: F.478, E.482, L.483, N.525, P.526, S.527, L.530 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.482, A:N.525, A:S.527, A:N.1145 EDO.24: 4 residues within 4Å: Chain A: R.58, I.75, W.81, Y.231 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.58 Water bridges: A:Y.231 EDO.25: 6 residues within 4Å: Chain A: D.1142, L.1147, R.1159, Y.1161, T.1251, H.1253 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.1142, A:R.1159, A:R.1159, A:H.1253 EDO.26: 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.50: 7 residues within 4Å: Chain B: S.196, D.197, Y.213, R.221, Y.223, T.224, K.225 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.197, B:K.225 Water bridges: B:R.221 EDO.51: 4 residues within 4Å: Chain B: A.583, Y.584, F.711, T.712 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.712 Water bridges: B:D.620, B:D.620, B:S.710, B:T.712, B:T.712 EDO.52: 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, B:R.1075 EDO.53: 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 EDO.54: 7 residues within 4Å: Chain B: D.1142, L.1147, E.1151, R.1159, Y.1161, T.1251, H.1253 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.1142, B:R.1159, B:R.1159, B:H.1253 EDO.55: 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

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
A

B
B

Glycoside hydrolase family 31 alpha-glucosidase

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