Structure of PDB 8irf Chain d Binding Site BS05

Receptor Information
>8irf Chain d (length=341) Species: 32053 (Thermostichus vulcanus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RGWFDILDDWLKRDRFVFVGWSGILLFPCAYLALGGWLTGTTFVTSWYTH
GLASSYLEGCNFLTVAVSTPANSMGHSLLLLWGPEAQGDFTRWCQLGGLW
TFIALHGAFGLIGFMLRQFEIARLVGVRPYNAIAFSAPIAVFVSVFLIYP
LGQSSWFFAPSFGVAAIFRFLLFFQGFHNWTLNPFHMMGVAGVLGGALLC
AIHGATVENTLFQDGEGASTFRAFNPTQAEETYSMVTANRFWSQIFGIAF
SNKRWLHFFMLFVPVTGLWMSAIGVVGLALNLRSYDFISQEIRAAEDPEF
ETFYTKNLLLNEGIRAWMAPQDQPHENFVFPEEVLPRGNAL
Ligand information
Ligand IDPHO
InChIInChI=1S/C55H74N4O5/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/h13,26,28-33,37,41,51,56,59H,1,14-25,27H2,2-12H3/b34-26+,42-28-,43-29-,44-28-,45-30-,46-29-,47-30-,52-50-/t32-,33-,37+,41+,51-/m1/s1
InChIKeyCQIKWXUXPNUNDV-RCBXBCQGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCC1=C(c2cc3c(c(c([nH]3)cc4nc(c5c6c(c(c([nH]6)cc1n2)C)C(=O)C5C(=O)OC)C(C4C)CCC(=O)OCC=C(C)CCCC(C)CCCC(C)CCCC(C)C)C)C=C)C
CACTVS 3.370CCc1c(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
ACDLabs 12.01O=C(OC\C=C(/C)CCCC(C)CCCC(C)CCCC(C)C)CCC6c4nc(cc1c(c(\C=C)c(n1)cc5nc(cc3c(c2C(=O)C(c4c2n3)C(=O)OC)C)C(=C5C)CC)C)C6C
OpenEye OEToolkits 1.7.6CCC1=C(/c/2c/c3c(c(c([nH]3)/cc/4\nc(c5c6c(c(/c(/[nH]6)c/c1n2)C)C(=O)[C@@H]5C(=O)OC)[C@H]([C@@H]4C)CCC(=O)OC/C=C(\C)/CCC[C@H](C)CCC[C@H](C)CCCC(C)C)C)C=C)C
CACTVS 3.370CCc1c(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
FormulaC55 H74 N4 O5
NamePHEOPHYTIN A
ChEMBLCHEMBL3349047
DrugBank
ZINC
PDB chain8irf Chain a Residue 415 [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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PDB8irf Oxygen-evolving photosystem II structures during S1-S2-S3 transitions.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		A41 W48 G121 F125 Q129 N142 F146 P149 P275 L279
Binding residue
(residue number reindexed from 1)		A30 W37 G110 F114 Q118 N131 F135 P138 P264 L268
Annotation score1
Enzymatic activity
Enzyme Commision number 1.10.3.9: photosystem II.
Gene Ontology
Molecular Function
GO:0010242 oxygen evolving activity
GO:0016168 chlorophyll binding
GO:0016491 oxidoreductase activity
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:0009523 photosystem II
GO:0009579 thylakoid
GO:0016020 membrane
GO:0031676 plasma membrane-derived thylakoid membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8irf, PDBe:8irf, PDBj:8irf
PDBsum8irf
PubMed38297122
UniProtD0VWR8|PSBD_THEVL Photosystem II D2 protein (Fragment) (Gene Name=psbD)

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