SMTL ID : 8fxt.1

Escherichia coli periplasmic Glucose-Binding Protein glucose complex: Acrylodan conjugate attached at W183C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

monomer

Ligands

1 x YDM: 1-[6-(dimethylamino)naphthalen-2-yl]propan-1-one(Covalent)

YDM.1: 10 residues within 4Å: Chain A: Y.9, D.13, N.42, K.91, E.148, H.151, M.181, C.182 Ligands: GLC.2, BGC.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.148, A:M.181 Hydrogen bonds: A:K.91

1 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.2: 14 residues within 4Å: Chain A: Y.9, D.13, F.15, N.90, K.91, H.151, D.153, R.157, C.182, N.210, D.235, N.255 Ligands: YDM.1, BGC.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.90, A:D.153, A:R.157, A:R.157, A:N.210, A:D.235, A:N.255 Water bridges: A:D.13, A:F.15, A:C.182, A:D.211, A:D.235 Salt bridges: A:H.151, A:R.157

5 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.3: 3 residues within 4Å: Chain A: D.12, D.39, Q.41 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.41 BGC.4: 14 residues within 4Å: Chain A: Y.9, D.13, F.15, N.90, K.91, H.151, D.153, R.157, C.182, N.210, D.235, N.255 Ligands: YDM.1, GLC.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.90, A:D.153, A:R.157, A:R.157, A:N.210, A:D.235, A:D.235, A:N.255 Water bridges: A:D.13, A:F.15, A:C.182, A:D.211, A:D.235 Salt bridges: A:H.151, A:R.157 BGC.5: 6 residues within 4Å: Chain A: K.10, D.12, N.14, D.183, T.184, A.212 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.12, A:T.184, A:T.184, A:T.184 Water bridges: A:K.10, A:K.10, A:D.12, A:N.14, A:M.181, A:A.185 Salt bridges: A:K.10 BGC.6: 3 residues within 4Å: Chain A: K.188, D.189, D.192 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.188, A:K.188, A:D.189, A:D.192 Water bridges: A:A.185, A:D.189 BGC.7: 6 residues within 4Å: Chain A: D.120, K.124, G.296, D.298, D.300, N.301 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.120, A:D.120, A:D.120, A:G.296, A:D.298, A:N.301 Water bridges: A:D.120 Salt bridges: A:K.124

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 6 residues within 4Å: Chain A: D.133, N.135, D.137, Q.139, Q.141, E.204 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.133, A:D.137, A:Q.139, A:E.204, A:E.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Allert, M.J. et al., Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching. Commun Chem (2023)

Release Date

2023-08-30

Peptides

D-galactose/methyl-galactoside binding periplasmic protein MglB: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D-galactose/methyl-galactoside binding periplasmic protein MglB