Structure of PDB 5xdg Chain D Binding Site BS03

Receptor Information

>5xdg Chain D (length=400) Species: 107035 (Paenibacillus sp. A11-2)

HRALDVATELAKTFRVTVRERERAGGTPKAERDAIRRSGLLTLLISKERG
GLGESWPTVYEAIAEIASADASLGHLFGYHFSNFAYVDLFASPEQKARWY
PQAVRERWFLGNASSENNAHVLDWRVTATPLPDGSYEINGTKAFCSGSAD
ADRLLVFAVTSRDPNGDGRIVAALIPSDRAGVQVNGDWDSLGMRQTDSGS
VTFSGVVVYPDELLGTPGQVTDAFASGSKPSLWTPITQLIFTHLYLGIAR
GALEEAAHYSRSHSRPFTLAGVEKATEDPYVLAIYGEFAAQLQVAEAGAR
EVALRVQELWERNHVTPEQRGQLMVQVASAKIVATRLVIELTSRLYEAMG
ARAAASRQFGFDRFWRDARTHTLHDPVAYKIREVGNWFLNHRFPTPSFYS

Ligand information

• Ligand ID: 83U
• InChI: InChI=1S/C12H8OS/c13-14-11-7-3-1-5-9(11)10-6-2-4-8-12(10)14/h1-8H
• InChIKey: NGDPCAMPVQYGCW-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: O=[S]1c2ccccc2c3ccccc13
  OpenEye OEToolkits 2.0.6: c1ccc2c(c1)-c3ccccc3S2=O
• Formula: C12 H8 O S
• Name: dibenzothiophene 5-oxide
• ChEMBL: CHEMBL335280
• ZINC: ZINC000001688627
• PDB chain: 5xdg Chain D Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5xdg Crystal structures of TdsC, a dibenzothiophene monooxygenase from the thermophile Paenibacillus sp. A11-2, reveal potential for expanding its substrate selectivity.
• Resolution: 1.747 Å
• Binding residue (original residue number in PDB): Y93 N97 N126 S128 W247 H388 F412 Y413
• Binding residue (residue number reindexed from 1): Y79 N83 N112 S114 W233 H374 F398 Y399
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 1.14.14.21: dibenzothiophene monooxygenase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0004497 monooxygenase activity
• GO:0008470 3-methylbutanoyl-CoA dehydrogenase activity
• GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
• GO:0050660 flavin adenine dinucleotide binding

Biological Process

• GO:0006552 L-leucine catabolic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:5xdg, PDBe:5xdg, PDBj:5xdg
• PDBsum: 5xdg
• PubMed: 28768765
• UniProt: Q9LBX2