Structure of PDB 7ddq Chain M Binding Site BS08

Receptor Information
>7ddq Chain M (length=305) Species: 1185920 (Phaeovulum veldkampii DSM 11550) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EYQNIFTQVQVAGKPELGMVEGVNLENRTTGTTNWPILGWFGNAQLGPIY
LGTLGTMSLIFGAFWFFLVGVSFIIQADYSPALFLRELFRAGLFPPAPEY
GLSLSAPLMEGGLWLIASFFLMLSVLLWWARTYKRAADLGMGKHTAWAFA
GALWLMFVLSFFRPILMGSWSEAVPYGIFPHLDWTNNFSLTHGNLFYNPF
HGLSIAFLYGSTMLFAMHGATILAVSRLGGERELEQIVDRGTAAERAALF
WRWTMGFNATMEGIHRWGWWFAVLTPVTGGIGILLSGTVVEDWSVWAQVH
GYKAL
Ligand information
Ligand IDSPO
InChIInChI=1S/C41H60O/c1-34(2)20-14-23-37(5)26-17-29-38(6)27-15-24-35(3)21-12-13-22-36(4)25-16-28-39(7)30-18-31-40(8)32-19-33-41(9,10)42-11/h12-13,15-16,18-22,24-28,30-32H,14,17,23,29,33H2,1-11H3/b13-12+,24-15+,25-16+,30-18+,32-19+,35-21+,36-22-,37-26+,38-27+,39-28+,40-31+
InChIKeyFJOCMTHZSURUFA-KXCOHNEYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=CCCC(=CCCC(=CC=CC(=CC=CC=C(C)C=CC=C(C)C=CC=C(C)C=CCC(C)(C)OC)C)C)C)C
CACTVS 3.341COC(C)(C)C\C=C\C(C)=C\C=C\C(C)=C\C=C\C(C)=C/C=C/C=C(C)/C=C/C=C(\C)CC\C=C(/C)CCC=C(C)C
CACTVS 3.341COC(C)(C)CC=CC(C)=CC=CC(C)=CC=CC(C)=CC=CC=C(C)C=CC=C(C)CCC=C(C)CCC=C(C)C
ACDLabs 10.04O(C(C\C=C\C(=C\C=C\C(=C\C=C\C(=C/C=C/C=C(/C=C/C=C(\C)CC\C=C(/C)CC\C=C(/C)C)C)C)C)C)(C)C)C
OpenEye OEToolkits 1.5.0CC(=CCCC(=CCC/C(=C/C=CC(=CC=C\C=C(\C)/C=C/C=C(\C)/C=C/C=C(\C)/C=CCC(C)(C)OC)C)/C)C)C
FormulaC41 H60 O
NameSPHEROIDENE
ChEMBL
DrugBank
ZINCZINC000064446704
PDB chain7ddq Chain M Residue 406 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7ddq Cryo-EM structure of the photosynthetic RC-LH1-PufX supercomplex at 2.8-angstrom resolution.
Resolution2.84 Å
Binding residue
(original residue number in PDB)		F68 V71 G72 F75 W116 S120 F121 M124 M158 F159 L161 S162 V176 Y178 G179 I180 H183
Binding residue
(residue number reindexed from 1)		F66 V69 G70 F73 W114 S118 F119 M122 M156 F157 L159 S160 V174 Y176 G177 I178 H181
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0042314 bacteriochlorophyll binding
GO:0045156 electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity
GO:0046872 metal ion binding
Biological Process
GO:0009772 photosynthetic electron transport in photosystem II
GO:0015979 photosynthesis
GO:0019684 photosynthesis, light reaction
Cellular Component
GO:0016020 membrane
GO:0030077 plasma membrane light-harvesting complex
GO:0042717 plasma membrane-derived chromatophore membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7ddq, PDBe:7ddq, PDBj:7ddq
PDBsum7ddq
PubMed34134992
UniProtA0A2T4JIN0

[Back to BioLiP]