SMTL ID : 5ynd.1

Crystal structure of Pullulanase from Klebsiella pneumoniae complex at 1 mM gamma-cyclodextrin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

monomer

Ligands

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

GLC-GLC-GLC-GLC.1: 6 residues within 4Å: Chain A: Y.97, W.99, W.114, I.145, K.152, D.157 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.99, A:D.157

5 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: A.569, D.572, Y.574, D.912 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.569, A:Y.574, A:D.912, H2O.7, H2O.10 CA.3: 4 residues within 4Å: Chain A: D.500, L.501, E.506, E.587 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.500, A:L.501, A:E.506, A:E.587, H2O.2, H2O.6 CA.4: 3 residues within 4Å: Chain A: E.64, D.167, D.181 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.167, H2O.1 CA.5: 6 residues within 4Å: Chain A: D.1013, S.1020, D.1022, V.1025, D.1026, Q.1089 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.1013, A:S.1020, A:D.1022, A:V.1025 CA.6: 3 residues within 4Å: Chain A: E.652, D.733, R.734 No protein-ligand interaction detected (PLIP)

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

PEG.7: 7 residues within 4Å: Chain A: S.1048, L.1049, Q.1050, V.1069, A.1070, A.1071, G.1073 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.1048 PEG.8: 7 residues within 4Å: Chain A: W.727, D.753, R.756, P.764, Y.831, D.853, N.854 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.753, A:R.756, A:R.756, A:Y.831 Water bridges: A:E.725, A:Y.848

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: E.544, T.548, K.551, W.916, R.919, V.931 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.544, A:T.548 GOL.10: 7 residues within 4Å: Chain A: S.418, K.421, P.422, E.423, G.424, W.425, D.426 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.424, A:D.426, A:D.426 GOL.11: 7 residues within 4Å: Chain A: H.798, D.818, K.819, K.824, E.828, I.829, D.830 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.798, A:D.818, A:D.830 GOL.12: 2 residues within 4Å: Chain A: Y.578, D.579 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.579 Water bridges: A:Y.578 GOL.13: 2 residues within 4Å: Chain A: Q.1068, T.1076 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.1068, A:Q.1068 Water bridges: A:T.1040, A:T.1040

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saka, N. et al., Elucidation of the mechanism of interaction between Klebsiella pneumoniae pullulanase and cyclodextrin. Acta Crystallogr D Struct Biol (2018)

Release Date

2018-10-24

Peptides

DUF3372 domain-containing protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DUF3372 domain-containing protein

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