SMTL ID : 5cvy.1

The Structure of Bacillus pumilus GH48 in complex with cellobiose and cellohexaose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x BGC- BGC: beta-D-glucopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)

BGC-BGC.1: 11 residues within 4Å: Chain A: H.30, E.38, E.49, W.411, W.417, D.534, R.682, W.684 Ligands: EDO.11, EDO.19, NA.33 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.30, A:H.30, A:E.49 Water bridges: A:E.49, A:E.49

1 x BGC- BGC- BGC- BGC- BGC- BGC: beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)

BGC-BGC-BGC-BGC-BGC-BGC.2: 27 residues within 4Å: Chain A: A.105, T.106, L.121, W.150, F.176, Q.177, E.212, Q.214, Q.219, R.221, T.223, N.224, A.225, K.267, Y.268, W.295, Y.296, S.298, W.309, W.311, I.313, Y.322, V.402, Y.403 Ligands: EDO.11, NA.29, NA.39 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.214, A:Q.214, A:Q.214 Water bridges: A:T.106

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 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.17, H2O.22

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

MLI.4: 9 residues within 4Å: Chain A: Q.180, T.375, S.377, W.378, N.379, E.398, H.404 Ligands: MLI.5, GOL.22 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.378 Hydrogen bonds: A:Q.180, A:N.379, A:N.379 Water bridges: A:H.404 Salt bridges: A:H.404 MLI.5: 8 residues within 4Å: Chain A: W.378, R.389, E.398, D.399, A.400, H.404 Ligands: MLI.4, GOL.22 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.399, A:A.400 Water bridges: A:D.399, A:H.404 Salt bridges: A:R.389, A:R.389, A:H.404 MLI.6: 5 residues within 4Å: Chain A: S.2, N.3, K.4, H.697, N.701 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.3, A:N.3, A:K.4 Water bridges: A:H.697, A:H.697 Salt bridges: A:H.697, A:H.697

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

EDO.7: 4 residues within 4Å: Chain A: D.195, A.218, L.303, G.304 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.195 EDO.8: 5 residues within 4Å: Chain A: I.272, G.273, S.274, Y.281, D.394 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.273 EDO.9: 5 residues within 4Å: Chain A: V.184, W.185, P.406, D.594 Ligands: EDO.19 No protein-ligand interaction detected (PLIP) EDO.10: 6 residues within 4Å: Chain A: K.240, S.247, L.250, D.251, K.254, G.337 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.251, A:K.254 EDO.11: 7 residues within 4Å: Chain A: A.39, E.49, W.150, A.225 Ligands: BGC-BGC.1, BGC-BGC-BGC-BGC-BGC-BGC.2, NA.29 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.49, A:E.49 EDO.12: 5 residues within 4Å: Chain A: P.407, N.410, I.503, A.504, W.505 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.410, A:W.505 EDO.13: 6 residues within 4Å: Chain A: S.655, L.656, K.659, P.676, V.677, F.678 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.677 Water bridges: A:S.655, A:L.656, A:K.659 EDO.14: 5 residues within 4Å: Chain A: P.386, A.387, G.388, R.389, Q.508 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.389, A:Q.508 EDO.15: 4 residues within 4Å: Chain A: K.15, D.17, F.22, W.54 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.17 Water bridges: A:K.15, A:D.17, A:G.26 EDO.16: 5 residues within 4Å: Chain A: E.79, V.85, E.87, Y.146, K.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.79, A:E.87, A:K.255 EDO.17: 5 residues within 4Å: Chain A: K.80, Y.81, S.167, H.168 Ligands: NA.36 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.80, A:Y.81 Water bridges: A:E.25, A:S.167, A:H.168 EDO.18: 10 residues within 4Å: Chain A: V.361, Q.364, K.449, A.518, T.519, G.520, N.521 Ligands: GOL.23, NA.28, NA.34 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.449, A:K.449, A:T.519, A:G.520, A:N.521 Water bridges: A:T.519 EDO.19: 4 residues within 4Å: Chain A: R.592, D.594 Ligands: BGC-BGC.1, EDO.9 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.591, A:D.594 EDO.20: 5 residues within 4Å: Chain A: W.238, E.241, Y.427, K.431, R.698 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.427, A:R.698

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.21: 4 residues within 4Å: Chain A: E.358, Y.393, W.512, G.514 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.393 Water bridges: A:E.358, A:E.358, A:Y.393, A:N.513 GOL.22: 8 residues within 4Å: Chain A: Q.180, S.377, W.378, N.379, E.398, H.404 Ligands: MLI.4, MLI.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.180, A:Q.180, A:S.377, A:N.379, A:N.379 Water bridges: A:V.402, A:V.402 GOL.23: 9 residues within 4Å: Chain A: V.361, S.445, K.449, F.515, A.518, T.519, G.520 Ligands: EDO.18, NA.28 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.445, A:K.449 Water bridges: A:K.449 GOL.24: 5 residues within 4Å: Chain A: N.156, P.166, S.167, H.168, K.169 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.156 Water bridges: A:N.162, A:S.167

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

NA.25: 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 NA.26: 3 residues within 4Å: Chain A: P.464, S.466, P.531 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.464, A:S.466 NA.27: 2 residues within 4Å: Chain A: N.246, T.248 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.246, A:N.246, A:T.248 Water bridges: A:T.248 NA.28: 5 residues within 4Å: Chain A: V.361, Q.364, K.449 Ligands: EDO.18, GOL.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.449, A:K.449 NA.29: 4 residues within 4Å: Chain A: D.227, Y.322 Ligands: BGC-BGC-BGC-BGC-BGC-BGC.2, EDO.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.322 Water bridges: A:E.49 NA.30: 2 residues within 4Å: Chain A: E.38, F.176 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.38 NA.31: 4 residues within 4Å: Chain A: S.332, S.333, E.350, L.353 4 PLIP interactions: 4 interactions with chain A Water bridges: A:S.332, A:E.350, A:E.350, A:E.350 NA.32: 5 residues within 4Å: Chain A: E.79, K.80, I.83, V.85, E.92 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.85, A:E.92 NA.33: 3 residues within 4Å: Chain A: E.590, R.592 Ligands: BGC-BGC.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.590 NA.34: 4 residues within 4Å: Chain A: W.362, D.510, N.521 Ligands: EDO.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.510, A:N.521, A:N.521 Water bridges: A:T.519 NA.35: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.251 Water bridges: A:K.255 NA.36: 6 residues within 4Å: Chain A: E.25, Y.81, S.167, H.168, K.169 Ligands: EDO.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.81, A:S.167, A:K.169 NA.37: 2 residues within 4Å: Chain A: N.452, T.484 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.367 Water bridges: A:Y.453, A:N.485 NA.38: 3 residues within 4Å: Chain A: Y.42, D.155, W.157 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.42, A:D.155, A:D.155 NA.39: 5 residues within 4Å: Chain A: M.206, T.210, E.212, P.216 Ligands: BGC-BGC-BGC-BGC-BGC-BGC.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.212, A:Q.219 Water bridges: A:T.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brunecky, R. et al., Natural diversity of glycoside hydrolase family 48 exoglucanases: insights from structure. Biotechnol Biofuels (2017)

Release Date

2016-08-10

Peptides

Glycoside hydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycoside hydrolase

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