SMTL ID : 6jfx.1

Crystal structure of Pullulanase from Paenibacillus barengoltzii complex with maltopentaose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

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

GLC-GLC-GLC.1: 13 residues within 4Å: Chain A: F.315, L.351, W.381, M.383, D.409, R.412, I.419, F.420, D.470, 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.527 Water bridges: A:F.315 GLC-GLC-GLC.3: 9 residues within 4Å: Chain A: R.495, D.546, S.549, Y.550, S.553, F.627, G.628, G.629, E.630 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.553, A:G.628, A:G.629, A:E.630 Water bridges: A:S.553

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: E.399, P.402 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.399 GOL.5: 3 residues within 4Å: Chain A: E.77, R.104, W.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.77, A:W.111

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

PEG.6: 5 residues within 4Å: Chain A: F.26, Y.304, K.305, A.306, R.308 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.304 PEG.7: 4 residues within 4Å: Chain A: N.447, Y.448, G.449, R.573 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.447 PEG.8: 4 residues within 4Å: Chain A: V.625, G.629, V.632, L.633 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.629

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

PGE.9: 5 residues within 4Å: Chain A: L.66, V.75, K.76, V.92, E.94 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.76

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.10: 2 residues within 4Å: Chain A: K.106, E.109 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.106, A:E.109 Water bridges: A:D.16, A:D.16 TRS.11: 4 residues within 4Å: Chain A: R.364, D.368, P.372, G.403 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.364, A:P.372, A:G.403 Water bridges: A:R.364, A:R.364, A:R.364

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.12: 3 residues within 4Å: Chain A: Q.146, H.270, A.271 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.13: 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.2, H2O.14

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

CL.14: 3 residues within 4Å: Chain A: G.288, G.317, N.318 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: Q.454, F.455 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain A: M.382, M.383, K.389, R.392, N.394 Ligand excluded by PLIP CL.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain A: A.114, V.115, K.295 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain A: H.561, R.626 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain A: R.164, K.179, L.227, H.231, S.247 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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