SMTL ID : 2yoc.1

Crystal structure of PulA from Klebsiella oxytoca

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.88 Å

Oligo State

homo-tetramer

Ligands

16 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: S.376, D.469, L.470, E.475, E.556 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.469, A:L.470, A:E.475, A:E.556, H2O.4 CA.2: 5 residues within 4Å: Chain A: T.472, A.538, D.541, Y.543, D.881 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:A.538, A:D.541, A:Y.543 CA.3: 6 residues within 4Å: Chain A: D.982, S.989, D.991, L.994, D.995, Q.1058 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.982, A:D.991, A:L.994 CA.4: 4 residues within 4Å: Chain A: E.621, E.627, D.702, R.703 No protein-ligand interaction detected (PLIP) CA.9: 5 residues within 4Å: Chain B: S.376, D.469, L.470, E.475, E.556 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.469, B:L.470, B:E.475, B:E.556 CA.10: 5 residues within 4Å: Chain B: T.472, A.538, D.541, Y.543, D.881 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:A.538, B:D.541 CA.11: 5 residues within 4Å: Chain B: D.982, S.989, D.991, L.994, Q.1058 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.982, B:S.989, B:D.991, B:L.994 CA.12: 4 residues within 4Å: Chain B: E.621, Q.700, D.702, R.703 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.702 CA.23: 5 residues within 4Å: Chain C: S.376, D.469, L.470, E.475, E.556 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.469, C:L.470, C:E.475, C:E.556, H2O.16 CA.24: 5 residues within 4Å: Chain C: T.472, A.538, D.541, Y.543, D.881 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:A.538, C:D.541, C:Y.543 CA.25: 6 residues within 4Å: Chain C: D.982, S.989, D.991, L.994, D.995, Q.1058 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.982, C:D.991, C:L.994 CA.26: 4 residues within 4Å: Chain C: E.621, E.627, D.702, R.703 No protein-ligand interaction detected (PLIP) CA.31: 5 residues within 4Å: Chain D: S.376, D.469, L.470, E.475, E.556 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.469, D:L.470, D:E.475, D:E.556 CA.32: 5 residues within 4Å: Chain D: T.472, A.538, D.541, Y.543, D.881 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:A.538, D:D.541 CA.33: 5 residues within 4Å: Chain D: D.982, S.989, D.991, L.994, Q.1058 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.982, D:S.989, D:D.991, D:L.994 CA.34: 4 residues within 4Å: Chain D: E.621, Q.700, D.702, R.703 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.702

28 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain A: Q.380, G.565, T.566 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: W.696, D.722, R.725, P.733 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain A: Y.547, D.548, C.631, C.632, Y.880 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: D.242, E.243, Q.246, R.325 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: Q.380, G.565, T.566 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain B: D.603, R.604, T.605 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain B: Q.288, T.295, R.297 Ligands: SO4.17 Ligand excluded by PLIP SO4.16: 8 residues within 4Å: Chain B: H.767, D.770, D.787, K.788, K.793, E.797, I.798, D.799 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain B: S.284 Ligands: SO4.15 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain B: K.390, P.391, D.392, K.570 Ligand excluded by PLIP SO4.19: 7 residues within 4Å: Chain B: F.964, R.965, N.966, T.967, E.1012 Chain C: D.154, R.157 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain B: R.961, G.987, A.988 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain B: T.405, K.406, D.954 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain B: K.713, A.781, S.796, G.806 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain C: Q.380, G.565, T.566 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain C: W.696, D.722, R.725, P.733 Ligand excluded by PLIP SO4.29: 5 residues within 4Å: Chain C: Y.547, D.548, C.631, C.632, Y.880 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain C: D.242, E.243, Q.246, R.325 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain D: Q.380, G.565, T.566 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain D: D.603, R.604, T.605 Ligand excluded by PLIP SO4.37: 4 residues within 4Å: Chain D: Q.288, T.295, R.297 Ligands: SO4.39 Ligand excluded by PLIP SO4.38: 8 residues within 4Å: Chain D: H.767, D.770, D.787, K.788, K.793, E.797, I.798, D.799 Ligand excluded by PLIP SO4.39: 2 residues within 4Å: Chain D: S.284 Ligands: SO4.37 Ligand excluded by PLIP SO4.40: 4 residues within 4Å: Chain D: K.390, P.391, D.392, K.570 Ligand excluded by PLIP SO4.41: 7 residues within 4Å: Chain A: D.154, R.157 Chain D: F.964, R.965, N.966, T.967, E.1012 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain D: R.961, G.987, A.988 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain D: T.405, K.406, D.954 Ligand excluded by PLIP SO4.44: 4 residues within 4Å: Chain D: K.713, A.781, S.796, G.806 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

East, A. et al., Structural Basis of Pullulanase Membrane Binding and Secretion Revealed by X-Ray Crystallography, Molecular Dynamics and Biochemical Analysis. Structure (2016)

Release Date

2013-11-06

Peptides

PULLULANASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

PULLULANASE