Structure of PDB 7pqd Chain M Binding Site BS05

Receptor Information
>7pqd Chain M (length=307) Species: 272943 (Cereibacter sphaeroides 2.4.1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AEYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPI
YLGSLGVLSLFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPE
YGLSFAAPLKEGGLWLIASFFMFVAVWSWWGRTYLRAQALGMGKHTAWAF
LSAIWLWMVLGFIRPILMGSWSEAVPYGIFSHLDWTNNFSLVHGNLFYNP
FHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIADRGTAAERAAL
FWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQN
HGMAPLN
Ligand information
Ligand IDSP2
InChIInChI=1S/C41H62O/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/h12-13,15-16,18,20-22,24-28,30-31H,14,17,19,23,29,32-33H2,1-11H3/b13-12-,24-15+,25-16+,30-18+,35-21+,36-22+,37-26+,38-27+,39-28+,40-31+
InChIKeyIUUXWKRRZDDNQG-DJSFQYKBSA-N
SMILES
SoftwareSMILES
CACTVS 3.341COC(C)(C)CCC\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
ACDLabs 10.04O(C(CCC\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(=CCCC(=CC=CC(=CC=CC=C(C)C=CC=C(C)C=CC=C(C)CCCC(C)(C)OC)C)C)C)C
OpenEye OEToolkits 1.5.0CC(=CCC/C(=C/CC/C(=C/C=C/C(=C/C=C\C=C(/C)\C=C\C=C(/C)\C=C\C=C(/C)\CCCC(C)(C)OC)/C)/C)/C)C
CACTVS 3.341COC(C)(C)CCCC(C)=CC=CC(C)=CC=CC(C)=CC=CC=C(C)C=CC=C(C)CCC=C(C)CCC=C(C)C
FormulaC41 H62 O
Name3,4-DIHYDROSPHEROIDENE
ChEMBL
DrugBank
ZINCZINC000064744265
PDB chain7pqd Chain M Residue 1005 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7pqd Cryo-EM structure of the dimeric Rhodobacter sphaeroides RC-LH1 core complex at 2.9 angstrom : the structural basis for dimerisation.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		F67 I70 G71 W75 F105 W115 S119 F120 M122 W157 G161 W171 V175 H182
Binding residue
(residue number reindexed from 1)		F67 I70 G71 W75 F105 W115 S119 F120 M122 W157 G161 W171 V175 H182
Annotation score1
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7pqd, PDBe:7pqd, PDBj:7pqd
PDBsum7pqd
PubMed34622934
UniProtQ3J1A6|RCEM_CERS4 Reaction center protein M chain (Gene Name=pufM)

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