Structure of PDB 5yq7 Chain M Binding Site BS04

Receptor Information
>5yq7 Chain M (length=305) Species: 120962 (Roseiflexus castenholzii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IDLHDEEYRDGLEGTIAKPPGHVGWMQRLLGEGQVGPIYVGLWGVISFIT
FFASAFIILVDYGRQVGWNPIIYLREFWNLAVYPPPTEYGLSWNVPWDKG
GAWLAATFFLHISVLTWWARLYTRAKATGVGTQLAWGFASALSLYFVIYL
FHPLALGNWSAAPGHGFRAILDWTNYVSIHWGNFYYNPFHMLSIFFLLGS
TLLLAMHGATIVATSKWKSEMEFTEMMAEGPGTQRAQLFWRWVMGWNANS
YNIHIWAWWFAAFTAITGAIGLFLSGTLVPDWYAWGETAKIVAPWPNPDW
AQYVF
Ligand information
Ligand IDMQE
InChIInChI=1S/C66H96O2/c1-50(2)26-16-27-51(3)28-17-29-52(4)30-18-31-53(5)32-19-33-54(6)34-20-35-55(7)36-21-37-56(8)38-22-39-57(9)40-23-41-58(10)42-24-43-59(11)44-25-45-60(12)48-49-62-61(13)65(67)63-46-14-15-47-64(63)66(62)68/h14-15,26,28,30,32,34,36,38,40,42,44,46-48H,16-25,27,29,31,33,35,37,39,41,43,45,49H2,1-13H3/b51-28+,52-30+,53-32+,54-34+,55-36+,56-38+,57-40+,58-42+,59-44+,60-48+
InChIKeyYYDMANIEKFAEJC-RYZSZPJESA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C(\C(=C\CC/C(C)=C/CC\C(=C\CC\C(=C\CC/C(C)=C/CC1=C(C(c2c(C1=O)cccc2)=O)C)C)C)C)C/C=C(/CC\C=C(\CC/C=C(/CC\C=C(\CC\C=C(\CC\C=C(\C)C)C)C)C)C)C
OpenEye OEToolkits 2.0.6CC1=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)CCC=C(C)CCC=C(C)C
OpenEye OEToolkits 2.0.6CC1=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)/CC/C=C(\C)/CC/C=C(\C)/CCC=C(C)C
CACTVS 3.385CC(C)=CCC/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\CC/C(C)=C/CC1=C(C)C(=O)c2ccccc2C1=O
CACTVS 3.385CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCC1=C(C)C(=O)c2ccccc2C1=O
FormulaC66 H96 O2
Name2-methyl-3-[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione;
Menaquinone 11
ChEMBL
DrugBank
ZINCZINC000150341901
PDB chain5yq7 Chain M Residue 701 [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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PDB5yq7 Cryo-EM structure of the RC-LH core complex from an early branching photosynthetic prokaryote.
Resolution4.1 Å
Binding residue
(original residue number in PDB)		M541 H542 W575 W581 A583
Binding residue
(residue number reindexed from 1)		M206 H207 W240 W246 A248
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0045156 electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity
Biological Process
GO:0009772 photosynthetic electron transport in photosystem II
GO:0019684 photosynthesis, light reaction

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5yq7, PDBe:5yq7, PDBj:5yq7
PDBsum5yq7
PubMed29674684
UniProtQ83XD0

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