SMTL ID : 6jeq.1

Crystal structure of Pullulanase from Paenibacillus barengoltzii complex with beta-cyclodextrin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

GLC-GLC-GLC-GLC-GLC-GLC-GLC.1: 4 residues within 4Å: Chain A: K.81, L.90, T.91 Ligands: IMD.4 No protein-ligand interaction detected (PLIP) GLC-GLC-GLC-GLC-GLC-GLC-GLC.2: 11 residues within 4Å: Chain A: W.381, M.383, D.409, R.412, D.413, D.418, I.419, F.420, I.421, N.471, E.524 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.524 Water bridges: A:D.470, A:N.525 GLC-GLC-GLC-GLC-GLC-GLC-GLC.3: 13 residues within 4Å: Chain A: R.495, D.546, S.549, Y.550, S.553, R.626, F.627, G.628, G.629, E.630 Ligands: IMD.5, IMD.6, PGE.7 No protein-ligand interaction detected (PLIP)

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

IMD.4: 3 residues within 4Å: Ligands: GLC-GLC-GLC-GLC-GLC-GLC-GLC.1, GLC-GLC-GLC-GLC-GLC-GLC-GLC.1, GLC-GLC-GLC-GLC-GLC-GLC-GLC.1 No protein-ligand interaction detected (PLIP) IMD.5: 2 residues within 4Å: Ligands: GLC-GLC-GLC-GLC-GLC-GLC-GLC.3, IMD.6 No protein-ligand interaction detected (PLIP) IMD.6: 5 residues within 4Å: Chain A: G.629, E.630 Ligands: GLC-GLC-GLC-GLC-GLC-GLC-GLC.3, GLC-GLC-GLC-GLC-GLC-GLC-GLC.3, IMD.5 No protein-ligand interaction detected (PLIP)

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

PGE.7: 5 residues within 4Å: Chain A: G.203, S.549, R.552, S.553 Ligands: GLC-GLC-GLC-GLC-GLC-GLC-GLC.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.552 PGE.8: 1 residues within 4Å: Chain A: E.624 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.624 PGE.9: 5 residues within 4Å: Chain A: A.560, P.562, P.598, D.599, R.626 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.599, A:R.626, A:R.626 Water bridges: A:D.599

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

PEG.10: 5 residues within 4Å: Chain A: E.489, A.492, H.631, G.665, V.666 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.666 Water bridges: A:E.489, A:E.489, A:R.664

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

CA.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.12: 4 residues within 4Å: Chain A: D.216, Y.217, E.224, E.245 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.216, A:Y.217, A:E.224, A:E.245, H2O.21

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

CL.13: 5 residues within 4Å: Chain A: M.382, M.383, K.389, R.392, N.394 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: R.164, K.179, 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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