Structure of PDB 6rqf Chain J Binding Site BS02

Receptor Information
>6rqf Chain J (length=160) Species: 3562 (Spinacia oleracea) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MGVTKKPDLNDPVLRAKLAKGMGHNYYGEPAWPNDLLYIFPVVILGTIAC
NVGLAVLEPSMIGEPADPFATPLEILPEWYFFPVFQILRTVPNKLLGVLL
MASVPAGLLTVPFLENVNKFQNPFRRPVATTVFLVGTVVALWLGIGATLP
IDKSLTLGLF
Ligand information
Ligand IDCLA
InChIInChI=1S/C55H73N4O5.Mg/c1-13-39-35(8)42-28-44-37(10)41(24-25-48(60)64-27-26-34(7)23-17-22-33(6)21-16-20-32(5)19-15-18-31(3)4)52(58-44)50-51(55(62)63-12)54(61)49-38(11)45(59-53(49)50)30-47-40(14-2)36(9)43(57-47)29-46(39)56-42;/h13,26,28-33,37,41,51H,1,14-25,27H2,2-12H3,(H-,56,57,58,59,61);/q-1;+2/p-1/b34-26+;/t32-,33-,37+,41+,51-;/m1./s1
InChIKeyATNHDLDRLWWWCB-AENOIHSZSA-M
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCC1=C(C2=Cc3c(c(c4n3[Mg]56[N]2=C1C=C7N5C8=C(C(C(=O)C8=C7C)C(=O)OC)C9=[N]6C(=C4)C(C9CCC(=O)OCC=C(C)CCCC(C)CCCC(C)CCCC(C)C)C)C)C=C)C
CACTVS 3.385CCC1=C(C)C2=Cc3n4[Mg][N]5C(=CC1=N2)C(=C6C(=O)[CH](C(=O)OC)C(=C56)C7=NC(=Cc4c(C)c3C=C)[CH](C)[CH]7CCC(=O)OCC=C(C)CCC[CH](C)CCC[CH](C)CCCC(C)C)C
ACDLabs 12.01O=C(OC)C1C(=O)C2=C(C)C3=CC=4C(CC)=C(C)C5=Cc6c(C=C)c(C)c7C=C8C(C)C(CCC(=O)OC\C=C(/C)CCCC(C)CCCC(C)CCCC(C)C)C=9C1=C2N3[Mg](n76)(N5=4)N8=9
OpenEye OEToolkits 2.0.7CCC1=C(C2=Cc3c(c(c4n3[Mg]56[N]2=C1C=C7N5C8=C([C@H](C(=O)C8=C7C)C(=O)OC)C9=[N]6C(=C4)[C@H]([C@@H]9CCC(=O)OC/C=C(\C)/CCC[C@H](C)CCC[C@H](C)CCCC(C)C)C)C)C=C)C
CACTVS 3.385CCC1=C(C)C2=Cc3n4[Mg][N@@]5C(=CC1=N2)C(=C6C(=O)[C@H](C(=O)OC)C(=C56)C7=NC(=Cc4c(C)c3C=C)[C@@H](C)[C@@H]7CCC(=O)OC\C=C(/C)CCC[C@H](C)CCC[C@H](C)CCCC(C)C)C
FormulaC55 H72 Mg N4 O5
NameCHLOROPHYLL A
ChEMBL
DrugBankDB02133
ZINC
PDB chain6rqf Chain I Residue 304 [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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PDB6rqf Cryo-EM structure of the spinach cytochrome b6f complex at 3.6 angstrom resolution.
Resolution3.58 Å
Binding residue
(original residue number in PDB)		Y80 L108 F133 G136 V139
Binding residue
(residue number reindexed from 1)		Y80 L108 F133 G136 V139
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0008121 ubiquinol-cytochrome-c reductase activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0045156 electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity
GO:0045158 electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity
Biological Process
GO:0006122 mitochondrial electron transport, ubiquinol to cytochrome c
GO:0009767 photosynthetic electron transport chain
GO:0015979 photosynthesis
GO:1902600 proton transmembrane transport
Cellular Component
GO:0005739 mitochondrion
GO:0009507 chloroplast
GO:0009535 chloroplast thylakoid membrane
GO:0009579 thylakoid
GO:0016020 membrane
GO:0042651 thylakoid membrane
GO:0045275 respiratory chain complex III

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6rqf, PDBe:6rqf, PDBj:6rqf
PDBsum6rqf
PubMed31723268
UniProtP00166|PETD_SPIOL Cytochrome b6-f complex subunit 4 (Gene Name=petD)

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