SMTL ID : 6jah.1

Crystal structure of ABC transporter alpha-glycoside-binding protein in complex with glucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

monomer

Ligands

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

GLC.1: 14 residues within 4Å: Chain A: T.46, D.70, V.71, D.118, Y.173, E.174, G.175, E.230, W.248, G.285, G.286, W.287, R.356 Ligands: EDO.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.70, A:D.118, A:Y.173, A:Y.173, A:G.286, A:G.286, A:W.287, A:R.356, A:R.356 Water bridges: A:E.230

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 5 residues within 4Å: Chain A: R.107, G.362, A.363, R.364, H.404 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.363 Hydrogen bonds: A:A.363, A:H.404 Water bridges: A:R.107, A:R.107, A:R.107, A:H.403, A:H.404 Salt bridges: A:R.107, A:R.107, A:R.364, A:H.404, A:H.404 CIT.3: 7 residues within 4Å: Chain A: E.375, R.383, K.384, D.392, A.395, R.396, R.399 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.383, A:D.392 Water bridges: A:S.378, A:S.378 Salt bridges: A:K.384, A:K.384, A:R.396, A:R.399

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 6 residues within 4Å: Chain A: F.116, D.118, W.248, Y.250, R.323 Ligands: GLC.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.118, A:R.323 Water bridges: A:D.11, A:D.11, A:D.11 EDO.5: 5 residues within 4Å: Chain A: E.17, R.20, W.21, R.320, L.321 No protein-ligand interaction detected (PLIP)

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

PEG.6: 4 residues within 4Å: Chain A: Y.307, E.312, V.313, D.316 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.307, A:D.316, A:R.320

1 x BA9: propane-2,2-diol(Non-covalent)

BA9.7: 4 residues within 4Å: Chain A: D.162, W.164, Y.228, V.236 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.162 Hydrogen bonds: A:D.162 Water bridges: A:N.241

1 x BA6: (2S)-heptane-1,2,7-triol(Non-covalent)

BA6.8: 5 residues within 4Å: Chain A: Y.311, E.312, K.315, D.333, R.334 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.311, A:K.315 Hydrogen bonds: A:R.334 Water bridges: A:K.315

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chandravanshi, M. et al., Structural and thermodynamic correlation illuminates the selective transport mechanism of disaccharide alpha-glycosides through ABC transporter. Febs J. (2020)

Release Date

2019-10-30

Peptides

ABC transporter, periplasmic substrate-binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ABC transporter, periplasmic substrate-binding protein

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