Structure of PDB 4y9t Chain A Binding Site BS01

Receptor Information

>4y9t Chain A (length=321) Species: 311402 (Allorhizobium ampelinum S4)

TKGMVYYLVPTLLDEFQTGSVNALSMFLGQVGYEMKTLNADNKTDAQQSQ
MNDVIALKPAAIILAAVDFNALKPSIEAARAAGIPVVEFDRQITSTPSDF
TSVAGTVEIGHIAGDHAISLLKGKNGDVKGKILQVPGDPGDPYTLDIQKG
FEEKIKAFPGVKIISVPAVQWEASAAGTIVSDQMLANPDIDLIFLHAAHL
SVAAVASLEAAGKKPGDVMLMSSNGAPVGLDLIRKGWLNVEVEQPLYAQA
AAIAMFMDKVVGKKPIKAGDYDVLGLKSVVTMETWGPNIKIPGSAITKEN
VDNPSFWGNLKPPTAAIKSVE

Ligand information

• Ligand ID: PA1
• InChI: InChI=1S/C6H13NO5/c7-3-5(10)4(9)2(1-8)12-6(3)11/h2-6,8-11H,1,7H2/t2-,3-,4-,5-,6+/m1/s1
• InChIKey: MSWZFWKMSRAUBD-UKFBFLRUSA-N
• SMILES:
  CACTVS 3.341: N[C@H]1[C@@H](O)O[C@H](CO)[C@@H](O)[C@@H]1O
  CACTVS 3.341: N[CH]1[CH](O)O[CH](CO)[CH](O)[CH]1O
  OpenEye OEToolkits 1.5.0: C(C1C(C(C(C(O1)O)N)O)O)O
  OpenEye OEToolkits 1.5.0: C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)N)O)O)O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1N)CO
• Formula: C6 H13 N O5
• Name: 2-amino-2-deoxy-alpha-D-glucopyranose;
  alpah-D-glucosamine;
  2-amino-2-deoxy-alpha-D-glucose;
  2-amino-2-deoxy-D-glucose;
  2-amino-2-deoxy-glucose
• ChEMBL: CHEMBL606759
• ZINC: ZINC000003860469
• PDB chain: 4y9t Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4y9t Structure of an ABC transporter solute-binding protein specific for the amino sugars glucosamine and galactosamine.
• Resolution: 1.801 Å
• Binding residue (original residue number in PDB): D39 F41 Q42 D115 R116 D166 Y168 W196 N249 Q269
• Binding residue (residue number reindexed from 1): D14 F16 Q17 D90 R91 D141 Y143 W171 N224 Q244
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0030246 carbohydrate binding

Cellular Component

• GO:0042597 periplasmic space

External links

• PDB: RCSB:4y9t, PDBe:4y9t, PDBj:4y9t
• PDBsum: 4y9t
• PubMed: 27303900
• UniProt: B9K0Q5