SMTL ID : 8ip1.1

Escherichia coli OpgD mutant-D388N with beta-1,2-glucan

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-dimer

Ligands

1 x BGC- BGC- BGC- BGC- BGC- BGC- BGC- BGC- BGC- BGC- BGC: beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose

BGC-BGC-BGC-BGC-BGC-BGC-BGC-BGC-BGC-BGC-BGC.1: 38 residues within 4Å: Chain A: P.78, N.82, F.106, M.110, F.112, R.162, R.172, D.173, S.176, L.178, G.179, A.180, Y.182, R.184, Y.190, Q.191, Y.192, S.195, R.197, T.203, E.209, F.211, T.278, M.280, D.300, M.353, G.354, R.359, M.378, I.380, E.385, T.386, L.387, N.388, V.391 Chain B: G.440, W.441, E.445 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.172, A:Y.190, A:Y.192 Water bridges: A:D.173, A:D.173

1 x BGC- BGC- BGC- BGC- BGC- BGC- BGC- BGC- BGC- BGC- BGC- BGC- BGC: beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose

BGC-BGC-BGC-BGC-BGC-BGC-BGC-BGC-BGC-BGC-BGC-BGC-BGC.2: 38 residues within 4Å: Chain A: G.440, W.441, E.445 Chain B: N.82, F.106, M.110, F.112, R.162, R.171, R.172, D.173, S.176, L.178, G.179, A.180, Y.182, R.184, Y.190, Q.191, Y.192, S.195, R.197, T.203, E.209, F.211, T.278, M.280, D.300, M.353, G.354, R.359, M.378, I.380, E.385, T.386, L.387, N.388, V.391 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.171, B:R.171, B:R.172, B:R.172

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 4 residues within 4Å: Chain A: K.450, K.484, Q.485, Y.504 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.485, A:Q.485 PEG.4: 7 residues within 4Å: Chain A: H.55, A.58, Q.59, Y.264, A.265, G.403, E.405 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.59, A:G.403, A:E.405

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 11 residues within 4Å: Chain B: K.165, V.174, V.186, D.187, D.188, Y.190, C.250, E.251, K.252, Q.254, V.255 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Motouchi, S. et al., Identification of enzymatic functions of osmo-regulated periplasmic glucan biosynthesis proteins from Escherichia coli reveals a novel glycoside hydrolase family. Commun Biol (2023)

Release Date

2024-03-13

Peptides

Glucans biosynthesis protein D: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glucans biosynthesis protein D

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