Structure of PDB 5ol2 Chain F Binding Site BS04

Receptor Information

>5ol2 Chain F (length=378) Species: 1496 (Clostridioides difficile)

MDLNSKKYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMM
GIPYPKEYGGEGGDTVGYIMAVEELSRVCGTTGVILSAHTSLGSWPIYQY
GNEEQKQKFLRPLASGEKLGAFGLTEPNAGTDASGQQTTAVLDGDEYILN
GSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFIVEKGTPGFSFGVKEKK
MGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIGIAAQAL
GLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQ
AAINKDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVER
MMRDAKITEIYEGTSEVQRMVISGKLLK

Ligand information

• Ligand ID: COS
• InChI: InChI=1S/C21H36N7O16P3S2/c1-21(2,16(31)19(32)24-4-3-12(29)23-5-6-49-48)8-41-47(38,39)44-46(36,37)40-7-11-15(43-45(33,34)35)14(30)20(42-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-31,48H,3-8H2,1-2H3,(H,23,29)(H,24,32)(H,36,37)(H,38,39)(H2,22,25,26)(H2,33,34,35)/t11-,14-,15-,16+,20-/m1/s1
• InChIKey: REVPHPVBPSIEKM-IBOSZNHHSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSS)O
  ACDLabs 10.04: O=C(NCCSS)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
  OpenEye OEToolkits 1.5.0: CC(C)(CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSS)O
  CACTVS 3.341: CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCSS
  CACTVS 3.341: CC(C)(CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCSS
• Formula: C21 H36 N7 O16 P3 S2
• Name: COENZYME A PERSULFIDE
• DrugBank: DB04036
• ZINC: ZINC000085432299
• PDB chain: 5ol2 Chain F Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ol2 The semiquinone swing in the bifurcating electron transferring flavoprotein/butyryl-CoA dehydrogenase complex from Clostridium difficile.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): L238 R242 E362 G363
• Binding residue (residue number reindexed from 1): L238 R242 E362 G363
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): L124 T125 G241 G374
• Catalytic site (residue number reindexed from 1): L124 T125 G241 G374
• Enzyme Commision number: 1.3.8.1: short-chain acyl-CoA dehydrogenase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003995 acyl-CoA dehydrogenase activity
• GO:0016491 oxidoreductase activity
• GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
• GO:0016937 short-chain fatty acyl-CoA dehydrogenase activity
• GO:0046872 metal ion binding
• GO:0050660 flavin adenine dinucleotide binding

External links

• PDB: RCSB:5ol2, PDBe:5ol2, PDBj:5ol2
• PDBsum: 5ol2
• PubMed: 29146947
• UniProt: A0A125V4E7