SMTL ID : 6j33.2 (1 other biounit)

Crystal structure of ligand-free of PulA from Klebsiella pneumoniae

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

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

MG.1: 5 residues within 4Å: Chain A: S.358, D.451, L.452, E.457, E.538 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.451, A:L.452, A:E.457, A:E.538, H2O.11, H2O.17 MG.2: 5 residues within 4Å: Chain A: D.964, S.971, D.973, V.976, Q.1040 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.964, A:S.971, A:D.973, A:V.976, H2O.11 MG.3: 3 residues within 4Å: Chain A: D.118, T.120, D.132 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.118, A:D.118, A:T.120, A:D.132, A:D.132 MG.4: 1 residues within 4Å: Chain A: R.685 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain A: S.974 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.974, H2O.15, H2O.45, H2O.46 MG.6: 2 residues within 4Å: Chain A: D.889, S.892 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.889, A:S.892, H2O.43, H2O.46, H2O.46 MG.7: 1 residues within 4Å: Chain A: S.75 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.75, H2O.44, H2O.46 MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain A: S.274, G.275, G.318, G.319 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.274, H2O.29, H2O.29 MG.10: 1 residues within 4Å: Chain A: S.459 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.11: 4 residues within 4Å: Chain A: A.520, D.523, Y.525, D.863 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.520, A:D.523, A:Y.525, H2O.20, H2O.26

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.12: 4 residues within 4Å: Chain A: R.139, A.140, G.143, V.144 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.144 Water bridges: A:R.339, A:R.339, A:R.339 ACT.13: 1 residues within 4Å: Chain A: S.369 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.369 Water bridges: A:S.369, A:S.369 ACT.14: 3 residues within 4Å: Chain A: Q.409, V.411, P.412 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.413, A:E.426, A:E.426 ACT.15: 3 residues within 4Å: Chain A: W.678, R.707, P.715 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.704 Salt bridges: A:R.707 ACT.16: 1 residues within 4Å: Chain A: T.499 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.499 Water bridges: A:K.502, A:K.502 Salt bridges: A:K.502

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saka, N. et al., Relationship between the induced-fit loop and the activity of Klebsiella pneumoniae pullulanase. Acta Crystallogr D Struct Biol (2019)

Release Date

2019-09-18

Peptides

pullulanase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

pullulanase

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