Structure of PDB 5xdc Chain D Binding Site BS01

Receptor Information

>5xdc Chain D (length=396) Species: 107035 (Paenibacillus sp. A11-2)

DHRALDVATELAKTFRVTVRERERAGGTPKAERDAIRRSGLLTLLISKER
GGLGESWPTVYEAIAEIASADASLGHLFGYHFSNFAYVDLFASPEQKARW
YPQAVRERWFLGNASSELDWRVTATPLPDGSYEINGTKAFCSGSADADRL
LVFAVTSRDPNGDGRIVAALIPSDRAGVQVNGDWDSLGMRQTDSGSVTFS
GVVVYPDELLGTPGQVTDAFASGSKPSLWTPITQLIFTHLYLGIARGALE
EAAHYSRSHSRPFTLAGVEKATEDPYVLAIYGEFAAQLQVAEAGAREVAL
RVQELWERNHVTPEQRGQLMVQVASAKIVATRLVIELTSRLYEAMGARAA
ASRQFGFDRFWRDARTHTLHDPVAYKIREVGNWFLNHRFPTPSFYS

Ligand information

• Ligand ID: IND
• InChI: InChI=1S/C8H7N/c1-2-4-8-7(3-1)5-6-9-8/h1-6,9H
• InChIKey: SIKJAQJRHWYJAI-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [nH]1ccc2ccccc12
  OpenEye OEToolkits 1.5.0: c1ccc2c(c1)cc[nH]2
  ACDLabs 10.04: c1cccc2c1ccn2
• Formula: C8 H7 N
• Name: INDOLE
• ChEMBL: CHEMBL15844
• DrugBank: DB04532
• ZINC: ZINC000014516984
• PDB chain: 5xdc Chain D Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5xdc Crystal structures of TdsC, a dibenzothiophene monooxygenase from the thermophile Paenibacillus sp. A11-2, reveal potential for expanding its substrate selectivity.
• Resolution: 1.5785 Å
• Binding residue (original residue number in PDB): H89 F158 S212 H385 H388
• Binding residue (residue number reindexed from 1): H76 F140 S194 H367 H370
• Annotation score: 1

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:5xdc, PDBe:5xdc, PDBj:5xdc
• PDBsum: 5xdc
• PubMed: 28768765
• UniProt: Q9LBX2