Structure of PDB 5mdx Chain A Binding Site BS04

Receptor Information
>5mdx Chain A (length=307) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ESLMIPTLLTATSVFIIAFIAAPPVDIDGIREPVSGSLLYGNNIISGAII
PTSAAIGLHFYPIWEAASVDEWLYNGGPYELIVLHFLLGVACYMGREWEL
SFRLGMRPWIAVAYSAPVAAATAVFLIYPIGQGSFSDGMPLGISGTFNFM
IVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESA
NEGYRFGQEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGI
WFTALGISTMAFNLNGFNFNQSVVDSQGRVINTWADIINRANLGMEVMHE
RNAHNFP
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 A Residue 402 [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)
M183 Q187 I192 H198 V202 T286 I290
Binding residue
(residue number reindexed from 1)
M150 Q154 I159 H165 V169 T253 I257
Annotation score1
Enzymatic activity
Enzyme Commision number 1.10.3.9: photosystem II.
Gene Ontology
Molecular Function
GO:0003729 mRNA binding
GO:0005506 iron ion binding
GO:0005515 protein binding
GO:0009055 electron transfer activity
GO:0010242 oxygen evolving activity
GO:0016168 chlorophyll binding
GO:0016491 oxidoreductase activity
GO:0016682 oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor
GO:0045156 electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity
GO:0046872 metal ion binding
Biological Process
GO:0009635 response to herbicide
GO:0009772 photosynthetic electron transport in photosystem II
GO:0015979 photosynthesis
GO:0019684 photosynthesis, light reaction
GO:0051238 sequestering of metal ion
Cellular Component
GO:0009507 chloroplast
GO:0009523 photosystem II
GO:0009534 chloroplast thylakoid
GO:0009535 chloroplast thylakoid membrane
GO:0009536 plastid
GO:0009579 thylakoid
GO:0016020 membrane

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:5mdx, PDBe:5mdx, PDBj:5mdx
PDBsum5mdx
PubMed28604725
UniProtP83755|PSBA_ARATH Photosystem II protein D1 (Gene Name=psbA)

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