Structure of PDB 8j5k Chain 0 Binding Site BS08

Receptor Information

>8j5k Chain 0 (length=169) Species: 29205 (Stephanocyclus meneghinianus)

APPGLVGALPPVGFFDPAGFAAKASPEELSRYREVEIMHGRFAQLAVLGF
IIPEKCAYDGSFGDDFLAPTGRALEVFNTDPLWLGLTLAVISALETVRLI
ETEPGTRTDAKIESLGWRPKTESEYINYQVRELQQGRLAMLAFAGEVAQE
LVNDKPLLVNLQDSGFVSW

Ligand information

• Ligand ID: CLA
• InChI: InChI=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
• InChIKey: ATNHDLDRLWWWCB-AENOIHSZSA-M
• SMILES:
  OpenEye OEToolkits 2.0.7: CCC1=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 3.385: CCC1=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 12.01: O=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 2.0.7: CCC1=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 3.385: CCC1=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
• Formula: C55 H72 Mg N4 O5
• Name: CHLOROPHYLL A
• DrugBank: DB02133
• PDB chain: 8j5k Chain 0 Residue 310

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8j5k Structural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana.
• Resolution: 2.93 Å
• Binding residue (original residue number in PDB): R77 Q80 D145 A146 I148 W153 R154 Y161 Y164 Q165 E168
• Binding residue (residue number reindexed from 1): R41 Q44 D109 A110 I112 W117 R118 Y125 Y128 Q129 E132
• Annotation score: 4

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Nov 15 16:42:10 2024

A problem occurred in a Python script. Here is the sequence of function calls leading up to the error, in the order they occurred.

 /var/www/html/BioLiP/pdb.cgi in <module>()

   1435     title=pdb2title(pdbid)

   1436     if bs.startswith("BS"):

=> 1437         pubmed,uniprot=display_interaction(pdbid,asym_id,bs,title)

   1438     else:

   1439         if lig3:

pubmed = '', uniprot = '', display_interaction = <function display_interaction>, pdbid = '8j5k', asym_id = '0', bs = 'BS08', title = 'Structural insights into photosystem II supercom...nnae of a centric diatom Cyclotella meneghiniana.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='8j5k', asym_id='0', bs='BS08', title='Structural insights into photosystem II supercom...nnae of a centric diatom Cyclotella meneghiniana.')

   1295         display_ec(ec,csaOrig,csaRenu)

   1296     if go:

=> 1297         display_go(go,uniprot,pdbid,asym_id)

   1298     return pubmed,uniprot

   1299 

global display_go = <function display_go>, go = '0009765,0016020', uniprot = '', pdbid = '8j5k', asym_id = '0'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0009765,0016020', uniprot='', pdbid='8j5k', asym_id='0')

    480         '''.replace("$namespace_link",namespace_link

    481           ).replace("$namespace",namespace

=>  482           ).replace("$uniprot",u

    483         ))

    484         for l,(term,name) in enumerate(go2aspect[Aspect]):

u undefined

UnboundLocalError: local variable 'u' referenced before assignment
      args = ("local variable 'u' referenced before assignment",)
      with_traceback = <built-in method with_traceback of UnboundLocalError object>