SMTL ID : 6l0z.1

The crystal structure of Salmonella enterica sugar-binding protein MalE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 18 residues within 4Å: Chain A: N.12, D.14, K.15, W.62, A.63, D.65, R.66, E.111, N.150, E.153, P.154, Y.155, F.156, W.230, M.330, W.340 Ligands: 2ME.5, ASO.12 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.62, A:D.65, A:D.65, A:E.153, A:E.153, A:Y.155

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 5 residues within 4Å: Chain A: Q.310, L.311, K.313, D.314, P.315 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.313, A:D.314 Hydrogen bonds: A:Q.310

4 x 2ME: METHOXYETHANE(Non-covalent)

2ME.3: 6 residues within 4Å: Chain A: R.344, T.345, I.348, N.349, R.354 Ligands: 2ME.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.345 2ME.4: 8 residues within 4Å: Chain A: Y.90, F.92, V.110, A.301, V.302, Q.308, M.321, Q.325 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.90, A:A.301 Water bridges: A:Q.308 2ME.5: 10 residues within 4Å: Chain A: N.12, K.42, E.44, W.62, E.153 Ligands: GLC-GLC.1, GLC-GLC.1, MG.9, ASO.10, ASO.12 No protein-ligand interaction detected (PLIP) 2ME.6: 4 residues within 4Å: Chain A: R.344, I.348 Ligands: 2ME.3, ASO.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.344

3 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain A: L.76, K.102, I.104 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain A: Q.152, R.344, I.348 Ligands: ASO.11 No protein-ligand interaction detected (PLIP) MG.9: 7 residues within 4Å: Chain A: N.12, K.42, L.43, E.44, W.62 Ligands: 2ME.5, ASO.10 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.44, H2O.1

3 x ASO: 1,5-anhydro-D-glucitol(Non-covalent)

ASO.10: 11 residues within 4Å: Chain A: K.42, E.44, E.45, E.153, Y.341, R.344 Ligands: 2ME.5, MG.9, ASO.11, ASO.12, GOL.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.42, A:E.44 Water bridges: A:K.42 ASO.11: 6 residues within 4Å: Chain A: K.42, R.344 Ligands: 2ME.6, MG.8, ASO.10, GOL.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.42, A:R.344 ASO.12: 13 residues within 4Å: Chain A: E.44, E.45, W.62, R.66, E.153, P.154, S.337, W.340, Y.341, R.344 Ligands: GLC-GLC.1, 2ME.5, ASO.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.44, A:E.45, A:R.66, A:R.66 Water bridges: A:D.65, A:S.337

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.13: 7 residues within 4Å: Chain A: K.15, G.16, Y.17, N.18, G.19, D.296, K.297 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.17, A:Y.17, A:Y.17, A:N.18, A:N.18, A:D.296, A:D.296, A:K.297 TRS.14: 7 residues within 4Å: Chain A: L.121, V.122, P.123, L.135, E.138, L.139, K.142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.121

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 9 residues within 4Å: Chain A: H.64, D.95, A.96, Y.176, I.329, M.330, P.331, N.332, I.333 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.176, A:N.332, A:N.332 Water bridges: A:N.332 GOL.16: 5 residues within 4Å: Chain A: K.42, E.45, Y.341 Ligands: ASO.10, ASO.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.42, A:E.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., The crystal structure of Salmonella enterica sugar-binding protein MalE. To Be Published

Release Date

2019-10-16

Peptides

Maltodextrin-binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Maltodextrin-binding protein

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