SMTL ID : 5ns6.1

Crystal structure of beta-glucosidase BglM-G1 from marine metagenome

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: D.265, K.269, K.271 9 PLIP interactions: 9 interactions with chain A Water bridges: A:D.265, A:K.269, A:K.269, A:K.269, A:K.269, A:K.271, A:E.354 Salt bridges: A:K.269, A:K.271 SO4.2: 4 residues within 4Å: Chain A: L.80, W.83, P.440 Chain C: E.123 No protein-ligand interaction detected (PLIP) SO4.3: 4 residues within 4Å: Chain A: E.123 Chain B: L.80, W.83, P.440 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.123 Water bridges: A:E.123, A:E.123 SO4.4: 1 residues within 4Å: Chain A: K.437 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.437 SO4.5: 2 residues within 4Å: Chain A: R.308, H.340 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.308, A:H.340 SO4.13: 3 residues within 4Å: Chain B: D.265, K.269, K.271 9 PLIP interactions: 9 interactions with chain B Water bridges: B:K.269, B:K.269, B:K.269, B:K.271, B:K.271, B:E.354, B:E.354 Salt bridges: B:K.269, B:K.271 SO4.14: 2 residues within 4Å: Chain B: R.308, H.340 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.308, B:H.340 SO4.15: 4 residues within 4Å: Chain B: Y.103, W.155, E.158 Ligands: GOL.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.158 SO4.25: 7 residues within 4Å: Chain C: I.286, H.287, P.288, G.289, D.290, M.291, E.292 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.289, C:M.291, C:E.292 SO4.26: 4 residues within 4Å: Chain B: E.123 Chain C: L.80, W.83, P.440 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.123 SO4.27: 2 residues within 4Å: Chain C: R.308, H.340 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.308 Salt bridges: C:R.308, C:H.340

23 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 9 residues within 4Å: Chain A: G.20, D.21, M.22, E.359, K.398, P.403, I.404, S.405 Chain C: W.19 Ligand excluded by PLIP GOL.7: 8 residues within 4Å: Chain A: Y.190, A.317, K.318, P.319, L.320, Y.322, K.323, Q.324 Ligand excluded by PLIP GOL.8: 3 residues within 4Å: Chain A: A.270, M.291, E.292 Ligand excluded by PLIP GOL.9: 11 residues within 4Å: Chain A: Q.33, H.134, W.135, N.178, E.179, N.304, Y.306, E.364, W.410, E.417, W.418 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain A: V.384, S.385, E.388, Y.446 Chain C: E.227, K.229 Ligand excluded by PLIP GOL.11: 10 residues within 4Å: Chain A: E.179, C.182, N.235, F.236, T.237, P.238, N.304, Y.305, Y.306, F.307 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain A: F.268, P.297, L.298, K.356, P.357, K.358 Ligand excluded by PLIP GOL.16: 3 residues within 4Å: Chain B: G.334, W.369, D.370 Ligand excluded by PLIP GOL.17: 9 residues within 4Å: Chain A: W.19 Chain B: G.20, D.21, M.22, E.359, K.398, P.403, I.404, S.405 Ligand excluded by PLIP GOL.18: 8 residues within 4Å: Chain B: Y.190, A.317, K.318, P.319, L.320, Y.322, K.323, Q.324 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain B: A.270, K.271, M.291, E.292 Ligand excluded by PLIP GOL.20: 11 residues within 4Å: Chain B: Q.33, H.134, W.135, N.178, E.179, N.304, Y.306, E.364, W.410, E.417, W.418 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain A: E.227, K.229 Chain B: V.384, S.385, E.388, Y.446 Ligand excluded by PLIP GOL.22: 9 residues within 4Å: Chain B: E.179, N.235, F.236, T.237, P.238, N.304, Y.305, Y.306, F.307 Ligand excluded by PLIP GOL.23: 6 residues within 4Å: Chain B: F.268, P.297, L.298, K.356, P.357, K.358 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain B: Y.103, G.104, E.158, K.162 Ligands: SO4.15 Ligand excluded by PLIP GOL.28: 3 residues within 4Å: Chain C: G.334, W.369, D.370 Ligand excluded by PLIP GOL.29: 8 residues within 4Å: Chain B: W.19 Chain C: D.21, M.22, E.359, K.398, P.403, I.404, S.405 Ligand excluded by PLIP GOL.30: 8 residues within 4Å: Chain C: Y.190, A.317, K.318, P.319, L.320, Y.322, K.323, Q.324 Ligand excluded by PLIP GOL.31: 11 residues within 4Å: Chain C: Q.33, H.134, W.135, N.178, E.179, N.304, Y.306, E.364, W.410, E.417, W.418 Ligand excluded by PLIP GOL.32: 6 residues within 4Å: Chain B: E.227, K.229 Chain C: V.384, S.385, E.388, Y.446 Ligand excluded by PLIP GOL.33: 9 residues within 4Å: Chain C: E.179, N.235, F.236, T.237, P.238, N.304, Y.305, Y.306, F.307 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain C: F.268, P.297, L.298, D.299, K.356, P.357, K.358 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mhaindarkar, D. et al., Loss of a conserved salt bridge in bacterial glycosyl hydrolase BgIM-G1 improves substrate binding in temperate environments. Commun Biol (2018)

Release Date

2018-08-08

Peptides

Beta-glucosidase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Beta-glucosidase