Structure of PDB 5xnl Chain 3 Binding Site BS12

Receptor Information
>5xnl Chain 3 (length=220) Species: 3888 (Pisum sativum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DLWYGPDRVKYLGPFSAQTPSYLTGEFPGDYGWDTAGLSADPEAFAKNRA
LEVIHGRWAMLGALGCITPEVLQKWVRVDFKEPVWFKAGSQIFSEGGLDY
LGNPNLVHAQSILAVLGFQIVLMGLVEGFRINGLPDVGEGNDLYPGGQYF
DPLGLADDPVTFAELKVKEIKNGRLAMFSMFGFFVQAIVTGKGPLENLLD
HLDNPVANNAWVYATKFVPG
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 chain5xnl Chain 3 Residue 610 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5xnl Structure and assembly mechanism of plant C2S2M2-type PSII-LHCII supercomplex
Resolution2.7 Å
Binding residue
(original residue number in PDB)		R79 M82 Y166 P167 G168 F172 A178 F184 L187 E191
Binding residue
(residue number reindexed from 1)		R57 M60 Y144 P145 G146 F150 A156 F162 L165 E169
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0016168 chlorophyll binding
GO:0019904 protein domain specific binding
Biological Process
GO:0009416 response to light stimulus
GO:0009635 response to herbicide
GO:0009644 response to high light intensity
GO:0009737 response to abscisic acid
GO:0009765 photosynthesis, light harvesting
GO:0009768 photosynthesis, light harvesting in photosystem I
GO:0009769 photosynthesis, light harvesting in photosystem II
GO:0010119 regulation of stomatal movement
GO:0015979 photosynthesis
Cellular Component
GO:0009507 chloroplast
GO:0009517 PSII associated light-harvesting complex II
GO:0009522 photosystem I
GO:0009523 photosystem II
GO:0009535 chloroplast thylakoid membrane
GO:0009579 thylakoid
GO:0009941 chloroplast envelope
GO:0010287 plastoglobule
GO:0016020 membrane
GO:0042651 thylakoid membrane

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5xnl, PDBe:5xnl, PDBj:5xnl
PDBsum5xnl
PubMed28839073
UniProtQ04918

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