Structure of PDB 7ymi Chain D Binding Site BS10

Receptor Information
>7ymi Chain D (length=323) Species: 329726 (Acaryochloris marina MBIC11017) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RGWFDVLDDWLKRDRFVFIGWSGILLFPCAFLSIGGWFTGTTFVTSWYTH
GLASSYLEGANFLTVAVSTPADSLGHSLLLLWGPEAQGDFTRWCQLGGLW
NFTTLHGVFGLIGFMLRQFEIARLVGVRPYNAVAFSGPIAVYVSVFLMYP
LGQSSWFFAPSWGVTSIFRFLLFAQGFHNLTLNPFHMMGVAGILGGALLC
AIHGATVENTLFEDETYSMVTANRFWSQIFGIAFSNKRWLHFFMLFVPVT
GLWASAIGLVGIALNMRAYDFVSQEIRAAEDPEFETFYTKNILLNEGLRA
WMAPQDQIHENFIFPEEVLPRGN
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 chain7ymi Chain D Residue 408 [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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PDB7ymi Structure of a large photosystem II supercomplex from Acaryochloris marina.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		L36 A40 G120 F124 Q128 A144 F145 P148 Y152 W172 G173 L278
Binding residue
(residue number reindexed from 1)		L26 A30 G110 F114 Q118 A134 F135 P138 Y142 W162 G163 L252
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:7ymi, PDBe:7ymi, PDBj:7ymi
PDBsum7ymi
PubMed38394197
UniProtB0C1V6|PSBD1_ACAM1 Photosystem II D2 protein 1 (Gene Name=psbD1)

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