Structure of PDB 5yq7 Chain L Binding Site BS04

Receptor Information
>5yq7 Chain L (length=309) Species: 120962 (Roseiflexus castenholzii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAVPRALPLPSGETLPAEAISSTGSQAASAEVIPFSIIEEFYKRPGKTLA
ARFFGVDPFDFWIGRFYVGLFGAISIIGIILGVAFYLYEGVVNEGTLNIL
AMRIEPPPVSQGLNVDPAQPGFFWFLTMVAATIAFVGWLLRQIDISLKLD
MGMEVPIAFGAVVSSWITLQWLRPIAMGAWGHGFPLGITHHLDWVSNIGY
QYYNFFYNPFHAIGITLLFASTLFLHMHGSAVLSEAKRNISDQNIHVFWR
NILGYSIGEIGIHRVAFWTGAASVLFSNLCIFLSGTFVKDWNAFWGFWDK
MPIWNGVGQ
Ligand information
Ligand IDBPH
InChIInChI=1S/C55H76N4O6/c1-13-39-34(7)41-29-46-48(38(11)60)36(9)43(57-46)27-42-35(8)40(52(58-42)50-51(55(63)64-12)54(62)49-37(10)44(59-53(49)50)28-45(39)56-41)23-24-47(61)65-26-25-33(6)22-16-21-32(5)20-15-19-31(4)18-14-17-30(2)3/h25,27-32,34-35,39-40,51,57,59H,13-24,26H2,1-12H3/b33-25+,41-29-,42-27-,43-27-,44-28-,45-28-,46-29-,52-50-/t31-,32-,34-,35+,39-,40+,51-/m1/s1
InChIKeyKWOZSBGNAHVCKG-SZQBJALDSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(OC\C=C(/C)CCCC(C)CCCC(C)CCCC(C)C)CCC6c4nc(cc1c(c(C(=O)C)c(n1)cc5nc(cc3c(c2C(=O)C(c4c2n3)C(=O)OC)C)C(CC)C5C)C)C6C
CACTVS 3.370CC[C@@H]1[C@@H](C)c2cc3[nH]c(cc4nc([C@@H](CCC(=O)OC\C=C(/C)CCC[C@H](C)CCC[C@H](C)CCCC(C)C)[C@@H]4C)c5[C@@H](C(=O)OC)C(=O)c6c(C)c([nH]c56)cc1n2)c(C)c3C(C)=O
OpenEye OEToolkits 1.7.6CCC1c2cc3c(c4c([nH]3)c(c5nc(cc6c(c(c([nH]6)cc(n2)C1C)C(=O)C)C)C(C5CCC(=O)OCC=C(C)CCCC(C)CCCC(C)CCCC(C)C)C)C(C4=O)C(=O)OC)C
OpenEye OEToolkits 1.7.6CCC1c2/cc\3/c(c4c([nH]3)c(c5n/c(c\c6c(c(c([nH]6)/cc(\n2)/C1C)C(=O)C)C)/C(C5CCC(=O)OC/C=C(\C)/CCCC(C)CCCC(C)CCCC(C)C)C)C(C4=O)C(=O)OC)C
CACTVS 3.370CC[CH]1[CH](C)c2cc3[nH]c(cc4nc([CH](CCC(=O)OCC=C(C)CCC[CH](C)CCC[CH](C)CCCC(C)C)[CH]4C)c5[CH](C(=O)OC)C(=O)c6c(C)c([nH]c56)cc1n2)c(C)c3C(C)=O
FormulaC55 H76 N4 O6
NameBACTERIOPHEOPHYTIN A
ChEMBL
DrugBank
ZINC
PDB chain5yq7 Chain L Residue 1003 [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)		I80 W139 A159 F160 L187 I189 G271
Binding residue
(residue number reindexed from 1)		I79 W138 A158 F159 L186 I188 G270
Annotation score4
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
Cellular Component
GO:0030077 plasma membrane light-harvesting complex

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

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