Structure of PDB 5c8l Chain B Binding Site BS01

Receptor Information

>5c8l Chain B (length=179) Species: 264462 (Bdellovibrio bacteriovorus HD100)

HLEEKTLSTRQIFKGRYLKIEQDQVQAPDGRTYTREYILHPGAAMMIPLL
PNGNVVMIHQYRHAVKKVFLEFPAGKRDHNEETLLTAKRELLEETGYEAK
DWKFLTTIHPVIGYSNEHIDLYLARDLTHLEQRLDQGQFIEVVEVKPADL
MQLVLEGKVSDVKTQIGAFWLDKFLRGEW

Ligand information

• Ligand ID: GLC
• InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1
• InChIKey: WQZGKKKJIJFFOK-DVKNGEFBSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C(C1C(C(C(C(O1)O)O)O)O)O
  OpenEye OEToolkits 1.5.0: C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)O
  CACTVS 3.341: OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
  CACTVS 3.341: OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@H]1O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)CO
• Formula: C6 H12 O6
• Name: alpha-D-glucopyranose;
  alpha-D-glucose;
  D-glucose;
  glucose
• ChEMBL: CHEMBL423707
• ZINC: ZINC000003861213
• PDB chain: 5c8l Chain B Residue 202

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5c8l Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): R64 G77 K78
• Binding residue (residue number reindexed from 1): R62 G75 K76
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): R64 A76 E92 E96 Q138
• Catalytic site (residue number reindexed from 1): R62 A74 E90 E94 Q136
• Enzyme Commision number: 3.6.1.13: ADP-ribose diphosphatase.

Gene Ontology

Molecular Function

• GO:0016787 hydrolase activity
• GO:0047631 ADP-ribose diphosphatase activity

Biological Process

• GO:0006753 nucleoside phosphate metabolic process
• GO:0019693 ribose phosphate metabolic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:5c8l, PDBe:5c8l, PDBj:5c8l
• PDBsum: 5c8l
• PubMed: 26524597
• UniProt: Q6MIH8