Structure of PDB 6lum Chain D Binding Site BS05

Receptor Information

>6lum Chain D (length=146) Species: 1445611 (Mycolicibacterium smegmatis MC2 51)

LGRPAPVMEREHDRPAALDHPRAPRKPRGIPYFEKYAWLFMRFSGIALVF
LALGHLFIMLMWQDGVYRIDFNYVAERWASPFWQIWDMALLWLAMIHGAN
GMRTIIGDYARKNVTKFWLNSLLLLATGFTLVLGSYVLVTFDANIS

Ligand information

• Ligand ID: MQ9
• InChI: InChI=1S/C56H80O2/c1-42(2)22-14-23-43(3)24-15-25-44(4)26-16-27-45(5)28-17-29-46(6)30-18-31-47(7)32-19-33-48(8)34-20-35-49(9)36-21-37-50(10)40-41-52-51(11)55(57)53-38-12-13-39-54(53)56(52)58/h12-13,22,24,26,28,30,32,34,36,38-40H,14-21,23,25,27,29,31,33,35,37,41H2,1-11H3/b43-24+,44-26-,45-28+,46-30+,47-32+,48-34+,49-36+,50-40+
• InChIKey: WCRXHNIUHQUASO-ABFXHILCSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC1=C(C(=O)c2ccccc2C1=O)CC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C
  CACTVS 3.341: CC(C)=CCCC(/C)=C/CCC(\C)=C/CCC(/C)=C/CCC(/C)=C/CCC(/C)=C/CCC(/C)=C/CCC(/C)=C/CCC(/C)=C/CC1=C(C)C(=O)c2ccccc2C1=O
  OpenEye OEToolkits 1.5.0: CC1=C(C(=O)c2ccccc2C1=O)C\C=C(/C)\CC\C=C(/C)\CC\C=C(/C)\CC\C=C(/C)\CC\C=C(/C)\CC\C=C(/C)\CC\C=C(\C)/CC\C=C(/C)\CCC=C(C)C
  ACDLabs 10.04: O=C2c1c(cccc1)C(=O)C(=C2C)C\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC/C=C(/C)CC\C=C(/C)CC\C=C(/C)C
  CACTVS 3.341: CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCC1=C(C)C(=O)c2ccccc2C1=O
• Formula: C56 H80 O2
• Name: MENAQUINONE-9
• ZINC: ZINC000098209188
• PDB chain: 6lum Chain N Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6lum Cryo-EM structure of trimeric Mycobacterium smegmatis succinate dehydrogenase with a membrane-anchor SdhF.
• Resolution: 2.84 Å
• Binding residue (original residue number in PDB): Q94 M98
• Binding residue (residue number reindexed from 1): Q84 M88
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding

Cellular Component

• GO:0016020 membrane

External links

• PDB: RCSB:6lum, PDBe:6lum, PDBj:6lum
• PDBsum: 6lum
• PubMed: 32843629
• UniProt: A0QT09