SMTL ID : 6jfj.1

Crystal structure of Pullulanase from Paenibacillus barengoltzii complex with maltohexaose and alpha-cyclodextrin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

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

GLC-GLC-GLC.1: 12 residues within 4Å: Chain A: F.315, L.351, W.381, M.383, D.409, R.412, I.419, F.420, N.471, N.525 Ligands: GLC-GLC-GLC.2, GLC-GLC-GLC.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.470, A:D.470 GLC-GLC-GLC.2: 16 residues within 4Å: Chain A: W.234, Y.236, D.237, H.284, F.315, C.316, R.348, D.350, L.351, E.379, H.469, D.470, N.525, Y.527 Ligands: GLC-GLC-GLC.1, GLC-GLC-GLC.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.220, A:D.237, A:D.237

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.3: 13 residues within 4Å: Chain A: R.495, D.546, S.549, Y.550, S.553, V.625, R.626, F.627, G.628, G.629, E.630 Ligands: PEG.16, PEG.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.626, A:G.629

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: N.361, K.400, P.402 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.361 GOL.5: 4 residues within 4Å: Chain A: K.559, A.560, P.562, R.565 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.559 Water bridges: A:A.560, A:R.565, A:R.565, A:G.596 GOL.6: 2 residues within 4Å: Chain A: E.399, V.457 No protein-ligand interaction detected (PLIP) GOL.7: 1 residues within 4Å: Chain A: A.151 No protein-ligand interaction detected (PLIP)

10 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 3 residues within 4Å: Chain A: T.20, G.21, K.29 No protein-ligand interaction detected (PLIP) PEG.9: 4 residues within 4Å: Chain A: N.447, Y.448, G.449, R.573 No protein-ligand interaction detected (PLIP) PEG.10: 5 residues within 4Å: Chain A: Q.146, K.147, H.270, A.271, G.273 No protein-ligand interaction detected (PLIP) PEG.11: 5 residues within 4Å: Chain A: G.205, T.207, G.273 Ligands: PEG.15, CL.34 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.273, A:K.559, A:K.559 PEG.12: 2 residues within 4Å: Chain A: G.629, V.632 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.629 PEG.13: 2 residues within 4Å: Chain A: G.450, Q.451 No protein-ligand interaction detected (PLIP) PEG.14: 4 residues within 4Å: Chain A: K.329, I.332, E.333, R.366 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.366 Water bridges: A:E.362 PEG.15: 5 residues within 4Å: Chain A: T.202, G.203, R.552, A.556 Ligands: PEG.11 No protein-ligand interaction detected (PLIP) PEG.16: 6 residues within 4Å: Chain A: E.630 Ligands: GLC-GLC-GLC-GLC-GLC.3, GLC-GLC-GLC-GLC-GLC.3, GLC-GLC-GLC-GLC-GLC.3, GLC-GLC-GLC-GLC-GLC.3, PEG.17 No protein-ligand interaction detected (PLIP) PEG.17: 5 residues within 4Å: Chain A: R.495, E.630 Ligands: GLC-GLC-GLC-GLC-GLC.3, GLC-GLC-GLC-GLC-GLC.3, PEG.16 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.491, A:R.495

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.18: 4 residues within 4Å: Chain A: V.75, K.76, V.92, E.94 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.76 PGE.19: 4 residues within 4Å: Chain A: W.475, R.540, A.543, H.544 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.540, A:R.540 Water bridges: A:W.475, A:R.491, A:D.537, A:D.537

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.20: 4 residues within 4Å: Chain A: F.26, K.305, R.308, R.324 No protein-ligand interaction detected (PLIP)

2 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.21: 3 residues within 4Å: Chain A: K.106, E.109 Ligands: IMD.23 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.106, A:K.106, A:E.109, A:E.109 TAM.22: 4 residues within 4Å: Chain A: F.63, E.77, R.104, W.111 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.63 Hydrogen bonds: A:E.77, A:R.104

4 x IMD: IMIDAZOLE(Non-functional Binders)(Non-covalent)

IMD.23: 1 residues within 4Å: Ligands: TAM.21 No protein-ligand interaction detected (PLIP) IMD.24: 6 residues within 4Å: Chain A: Y.448, R.573, A.574, H.575, L.576, R.577 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.574 IMD.25: 4 residues within 4Å: Chain A: D.368, E.369, I.370, P.372 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.370 IMD.26: 3 residues within 4Å: Chain A: D.432, G.433, F.434 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.432 pi-Stacking: A:F.434

2 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.27: 4 residues within 4Å: Chain A: D.216, Y.217, E.224, E.245 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.216, A:Y.217, A:E.224, A:E.245, H2O.3, H2O.5 CA.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.29: 5 residues within 4Å: Chain A: M.382, M.383, K.389, R.392, N.394 Ligand excluded by PLIP CL.30: 5 residues within 4Å: Chain A: R.164, K.179, L.227, H.231, S.247 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain A: H.593, R.600, R.675 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain A: R.424, K.425 Ligand excluded by PLIP CL.33: 4 residues within 4Å: Chain A: K.425, T.482, P.483, G.484 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain A: G.205, I.555, K.559 Ligands: PEG.11 Ligand excluded by PLIP CL.35: 2 residues within 4Å: Chain A: Q.454, F.455 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain A: A.612, L.633, R.664 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, P. et al., Structural basis of carbohydrate binding in domain C of a type I pullulanase from Paenibacillus barengoltzii. Acta Crystallogr D Struct Biol (2020)

Release Date

2019-02-20

Peptides

Pulullanase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Pulullanase

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