SMTL ID : 5vma.1

Structure of B. pumilus GH48 in complex with a cellobio-derived isofagomine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

2 x G2I: (3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl 4-O-beta-D-glucopyranosyl-beta-D-glucopyranoside(Non-covalent)

G2I.1: 18 residues within 4Å: Chain A: A.39, P.40, T.47, E.49, W.150, N.174, F.176, Q.177, T.223, N.224, A.225, D.227, W.295, Y.296, Y.322, V.402, Y.403 Ligands: G2I.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:W.150 Hydrogen bonds: A:E.49, A:E.49, A:E.49, A:W.150, A:N.174, A:T.223, A:N.224, A:D.227, A:Y.322 Water bridges: A:E.49, A:Y.296, A:Y.296, A:S.298, A:S.298, A:Y.322, A:Y.403 G2I.2: 15 residues within 4Å: Chain A: H.30, E.38, E.49, W.411, W.417, T.532, D.534, E.590, E.591, R.592, R.682, W.684 Ligands: G2I.1, EDO.8, EDO.17 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.38, A:E.49, A:D.534, A:D.534, A:W.684 Water bridges: A:T.532, A:E.591, A:R.682

1 x 9MR: (3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl beta-D-glucopyranoside(Non-covalent)

9MR.3: 8 residues within 4Å: Chain A: A.105, T.106, L.121, E.212, Q.219, Y.268, W.309, W.311 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.106, A:T.106, A:T.106, A:Q.219, A:Y.268 Water bridges: A:E.212, A:E.212

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: Q.181, E.186, D.405 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Q.181, A:E.186, A:D.405, H2O.6, H2O.16 CA.5: 5 residues within 4Å: Chain A: E.79, K.80, I.83, V.85, E.92 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.79, A:I.83, A:V.85, H2O.8, H2O.12

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 3 residues within 4Å: Chain A: N.165, P.166, S.167 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.165, A:S.167

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 3 residues within 4Å: Chain A: D.195, A.218, L.303 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.195 EDO.8: 5 residues within 4Å: Chain A: E.38, W.185, P.406, D.594 Ligands: G2I.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.185 EDO.9: 1 residues within 4Å: Chain A: R.565 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.565, A:R.565 EDO.10: 5 residues within 4Å: Chain A: P.386, A.387, G.388, R.389, Q.508 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.388, A:R.389, A:Q.508 EDO.11: 9 residues within 4Å: Chain A: Y.11, E.58, Y.61, G.62, D.67, W.68, S.69, K.70, L.71 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.11, A:E.58, A:W.68, A:K.70, A:L.71 EDO.12: 3 residues within 4Å: Chain A: L.455, I.458, I.460 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.455 Water bridges: A:I.460 EDO.13: 3 residues within 4Å: Chain A: N.610, G.621, S.622 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.621 EDO.14: 3 residues within 4Å: Chain A: K.15, G.26, W.54 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.15, A:D.17, A:N.77 EDO.15: 5 residues within 4Å: Chain A: F.599, S.639, A.641, D.642, K.648 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.599, A:S.639, A:K.648 EDO.16: 8 residues within 4Å: Chain A: W.362, D.510, T.511, W.512, S.517, A.518, T.519, N.521 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.517, A:T.519, A:G.520, A:N.521, A:N.521 Water bridges: A:N.513, A:N.513, A:N.513 EDO.17: 2 residues within 4Å: Chain A: S.408 Ligands: G2I.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.408 EDO.18: 4 residues within 4Å: Chain A: I.272, G.273, S.274, Y.281 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.272

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.19: 4 residues within 4Å: Chain A: Y.140, D.251, K.252, K.255 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.251 Water bridges: A:K.252 Salt bridges: A:K.252, A:K.255

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

ACT.20: 4 residues within 4Å: Chain A: L.8, H.12, Y.61, T.65 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.65 Salt bridges: A:H.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alahuhta, P.M. et al., Bacillus pumilus family 48 glycoside hydrolase in complex with cellobio-derived isofagomine. To Be Published

Release Date

2018-10-31

Peptides

Glycoside hydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycoside hydrolase

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