Structure of PDB 8f4k Chain d Binding Site BS08

Receptor Information
>8f4k Chain d (length=341) Species: 197221 (Thermosynechococcus vestitus BP-1) [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 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 chain8f4k Chain d Residue 403 [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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PDB8f4k Structural evidence for intermediates during O 2 formation in photosystem II.
Resolution2.16 Å
Binding residue
(original residue number in PDB)		V152 V156 F181 L182 F185 Q186 W191 H197 G200 V201 S282 A283 V286
Binding residue
(residue number reindexed from 1)		V141 V145 F170 L171 F174 Q175 W180 H186 G189 V190 S271 A272 V275
Annotation score1
Enzymatic activity
Enzyme Commision number 1.10.3.9: photosystem II.
Gene Ontology
Molecular Function
GO:0005506 iron ion binding
GO:0009055 electron transfer activity
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
GO:0042651 thylakoid membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8f4k, PDBe:8f4k, PDBj:8f4k
PDBsum8f4k
PubMed37138085
UniProtQ8CM25|PSBD_THEVB Photosystem II D2 protein (Gene Name=psbD1)

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