Structure of PDB 5xs8 Chain A Binding Site BS02

Receptor Information

>5xs8 Chain A (length=474) Species: 519441 (Streptobacillus moniliformis DSM 12112)

PKETTIFAMHLGKALDPNLPVFVKAEKDTNIKLVNVASQNQTDQIQAYNL
MLTEGKLPDIVSYELSADLENLGIEGGLIPLEDLINQHAPNLKKFFEENP
RYKKDAVAVDGHIYMIPNYYDYFNIKVSQGYFIRQDWLEKLGLKEPRTVD
ELYTTLKAFREKDPNGNGKKDEVPFFVRANNVRKVLTSLVDLFKASPIWY
EENGMVKYGPAQKEFKHAIKELSKWYKEGLIDEEIFTRGLESRDYLLSNN
LGGATDDWIASTSSYNRNLADKIPGFNLKLVLPYELNGNAKTRHARTTYL
GGWGISKDAKDPVSLIKYFDYWYSVEGRRLWNFGIEGSEYTLVDGKPVFT
DKVLKNPDGKTPLAVLREVGAQYRLGAFQDAQYELGWASESAKAGYKYYM
DNDVVLDELPILKYTKEKSKEFVSIDTAMRAVVEEKAQQWILGSGDIDKE
WDAYIKRLENLGLSKAEQIQNEAF

Ligand information

• Ligand ID: GCD
• InChI: InChI=1S/C6H8O6/c7-2-1-3(5(9)10)12-6(11)4(2)8/h1-2,4,6-8,11H,(H,9,10)/t2-,4+,6+/m0/s1
• InChIKey: IAKKJSVSFCTLRY-YKKSOZKNSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: C1=C(OC(C(C1O)O)O)C(=O)O
  CACTVS 3.370: O[C@@H]1OC(=C[C@H](O)[C@H]1O)C(O)=O
  CACTVS 3.370: O[CH]1OC(=C[CH](O)[CH]1O)C(O)=O
  OpenEye OEToolkits 1.7.6: C1=C(O[C@H]([C@@H]([C@H]1O)O)O)C(=O)O
  ACDLabs 12.01: O=C(O)C=1OC(O)C(O)C(O)C=1
• Formula: C6 H8 O6
• Name: 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid;
  4,5-DEHYDRO-D-GLUCURONIC ACID;
  4-deoxy-alpha-L-threo-hex-4-enuronic acid;
  4-deoxy-L-threo-hex-4-enuronic acid;
  4-deoxy-threo-hex-4-enuronic acid
• DrugBank: DB02305
• PDB chain: 5xs8 Chain E Residue 2

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5xs8 Alternative substrate-bound conformation of bacterial solute-binding protein involved in the import of mammalian host glycosaminoglycans.
• Resolution: 1.952 Å
• Binding residue (original residue number in PDB): W284 S287 L389 Q405 Y409 E410
• Binding residue (residue number reindexed from 1): W258 S261 L363 Q379 Y383 E384
• Annotation score: 4
• Binding affinity: PDBbind-CN: -logKd/Ki=5.41,Kd=3.86uM

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding

External links

• PDB: RCSB:5xs8, PDBe:5xs8, PDBj:5xs8
• PDBsum: 5xs8
• PubMed: 29208901
• UniProt: D1AWE0