Structure of PDB 5xnm Chain c Binding Site BS12

Receptor Information
>5xnm Chain c (length=450) Species: 3888 (Pisum sativum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TGRDQETTGFAWWAGNARLINLSGKLLGAHVAHAGLIVFWAGAMNLFEVA
HFVPEKPMYEQGLILLPHLATLGWGVGPGGEVIDTFPYFVSGVLHLISSA
VLGFGGIYHALLGPETLEESFPFFGYVWKDRNKMTTILGIHLILLGIGSF
LLVFKAFYFGGIYDTWAPGGGDVRKITNFTLSPSILFGYLLKSPFGGEGW
IVSVDDLEDIIGGHVWLGSICILGGIWHILTKPFAWARRALVWSGEAYLS
YSLGALAVFGFIACCFVWFNNTAYPSEFYGPTGPEASQAQAFTFLVRDQR
LGANVGSAQGPTGLGKYLMRSPTGEVIFGGETMRFWDLRAPWLEPLRGPN
GLDLSRLKKDIQPWQERRSAEYMTHAPLGSLNSVGGVATEINAVNYVSPR
SWLATSHFVLGFFLFVGHLWHAGRARAAAAGFEKGIDRDFEPVLSMTPLN
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 chain5xnm Chain c Residue 511 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5xnm Structure and assembly mechanism of plant C2S2M2-type PSII-LHCII supercomplex
Resolution3.2 Å
Binding residue
(original residue number in PDB)		W35 G38 N39 R41 L42 A52 F127 I130 L134
Binding residue
(residue number reindexed from 1)		W12 G15 N16 R18 L19 A29 F104 I107 L111
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
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:0009535 chloroplast thylakoid membrane
GO:0009579 thylakoid
GO:0016020 membrane

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5xnm, PDBe:5xnm, PDBj:5xnm
PDBsum5xnm
PubMed28839073
UniProtP06004|PSBC_PEA Photosystem II CP43 reaction center protein (Gene Name=psbC)

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