Structure of PDB 5mdx Chain c Binding Site BS09

Receptor Information
>5mdx Chain c (length=433) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AGRDQETTGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMNLFEVA
HFVPEKPMYEQGLILLPHLATLGWGVGPGGEVIDTFPYFVSGVLHLISSA
VLGFGGIYHALLGPETLEESFPFFGYVWKDRNKMTTILGIHLILLGVGAF
LLVFKALYFGGVYDTWAPGGGDVRKITNLTLSPSVIFGYLLKSPFGGEGW
IVSVDDLEDIIGGHVWLGSICIFGGIWHILTKPFAWARRALVWSGEAYLS
YSLAALSVCGFIACCFVWFNNTAYPSEFYGPTGPEASQAQAFTFLVRDQR
LGANVGSAQGPTGLGKYLMRSPTGEVIFGGETMRFWDLRAPWLEPLRGPN
GLDLSRLKKDIQPWQERRSAEYMTHAPVNYVSPRSWLSTSHFVLGFFLFV
GHLWHAGRARAAAAGFEKGIDRDFEPVLSMTPL
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 chain5mdx Chain c Residue 509 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5mdx Subunit and chlorophyll organization of the plant photosystem II supercomplex.
Resolution5.3 Å
Binding residue
(original residue number in PDB)		N39 I43 L49 H53 H56 L272 S275
Binding residue
(residue number reindexed from 1)		N16 I20 L26 H30 H33 L249 S252
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003729 mRNA binding
GO:0005515 protein binding
GO:0016168 chlorophyll binding
GO:0045156 electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity
GO:0046872 metal ion binding
Biological Process
GO:0009767 photosynthetic electron transport chain
GO:0009772 photosynthetic electron transport in photosystem II
GO:0015979 photosynthesis
GO:0019684 photosynthesis, light reaction
Cellular Component
GO:0005737 cytoplasm
GO:0009507 chloroplast
GO:0009521 photosystem
GO:0009523 photosystem II
GO:0009533 chloroplast stromal thylakoid
GO:0009534 chloroplast thylakoid
GO:0009535 chloroplast thylakoid membrane
GO:0009536 plastid
GO:0009539 photosystem II reaction center
GO:0009579 thylakoid
GO:0010287 plastoglobule
GO:0016020 membrane

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5mdx, PDBe:5mdx, PDBj:5mdx
PDBsum5mdx
PubMed28604725
UniProtP56778|PSBC_ARATH Photosystem II CP43 reaction center protein (Gene Name=psbC)

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