SMTL ID : 5bv9.1

The Structure of Bacillus pumilus GH48 in complex with cellobiose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

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

BGC-BGC.1: 8 residues within 4Å: Chain A: H.30, E.38, A.39, W.411, W.417, D.534, R.682, W.684 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.30, A:H.30

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 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.12, H2O.24 CA.3: 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.23 CA.4: 2 residues within 4Å: Chain A: N.246, T.248 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.248, H2O.19, H2O.26, H2O.28, H2O.34

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

MLI.5: 8 residues within 4Å: Chain A: Q.180, T.375, S.377, W.378, N.379, E.398, H.404 Ligands: MLI.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.378 Hydrogen bonds: A:Q.180, A:N.379, A:N.379 Water bridges: A:W.378, A:H.404 Salt bridges: A:H.404 MLI.6: 8 residues within 4Å: Chain A: W.378, R.389, E.398, D.399, A.400, H.404 Ligands: MLI.5, ACT.13 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.378 Hydrogen bonds: A:D.399, A:A.400 Water bridges: A:R.389, A:R.389, A:D.399 Salt bridges: A:R.389, A:R.389, A:H.404

3 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: A.105, T.106, L.121, Y.268, W.311 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.106, A:Y.268, A:Y.268 EDO.9: 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

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

ACT.10: 6 residues within 4Å: Chain A: Y.237, W.238, E.241, I.428, K.431, D.432 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:K.431 Hydrogen bonds: A:Y.237, A:E.241, A:D.432 Water bridges: A:Y.427, A:K.431 Salt bridges: A:K.431 ACT.11: 2 residues within 4Å: Chain A: R.565, D.568 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.568 Water bridges: A:A.569 ACT.12: 5 residues within 4Å: Chain A: S.2, N.3, K.4, H.697, N.701 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.3, A:N.3, A:K.4 Salt bridges: A:H.697 ACT.13: 5 residues within 4Å: Chain A: D.399, A.400, H.404 Ligands: MLI.6, GOL.18 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:H.404 Water bridges: A:H.404 Salt bridges: A:H.404 ACT.14: 4 residues within 4Å: Chain A: W.150, F.176, W.295, Y.403 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.150 Water bridges: A:W.295, A:Y.403 ACT.15: 4 residues within 4Å: Chain A: F.176, E.182, Y.403, D.405 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.176, A:Y.403 Hydrogen bonds: A:E.38 Water bridges: A:V.184

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.16: 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.17: 10 residues within 4Å: Chain A: V.361, W.362, Q.364, K.449, D.510, W.512, A.518, T.519, G.520, N.521 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.449, A:K.449, A:D.510, A:D.510, A:N.521 Water bridges: A:T.519 GOL.18: 5 residues within 4Å: Chain A: P.407, N.410, A.504, W.505 Ligands: ACT.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.410, A:I.503, A:W.505

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, M. et al., Strategies to reduce end-product inhibition in family 48 glycoside hydrolases. Proteins (2016)

Release Date

2015-09-30

Peptides

Cellulose 1,4-beta-cellobiosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cellulose 1,4-beta-cellobiosidase

Related Entries With Identical Sequence