Structure of PDB 8cmo Chain A Binding Site BS42

Receptor Information

>8cmo Chain A (length=740) Species: 75800 (Coelastrella)

KKVKIAVDRNPVETSFEKWAKPGHFSRTLSKGPNTTTWIWNLHADAHDFD
SHTSDLEEISRKVFSAHFGQLGVIFIWLSGMYFHGARFSNYEAWLSDPVH
IKPSAQVVWPVVGQEILNGDVGGGFQGIQITSGFFQLWRASGITSELQLY
TTAIGGLVMAAAMFFAGWFHYHKAAPKLEWFQNVESMLNHHLAGLLGLGS
LSWAGHQIHVSLPVNKLLDAGVDPKEIPLPHEFLLNRQIMQDLYPSFAKG
LAPFFTLQWGEYSDFLTFNGGLNPVTGGLWLSDTAHHHLAIAVLFLVAGH
MYRTNWGIGHSMKEILEAHKGPFTGEGHVGLYEILTTSWHAQLAINLALF
GSLSIIVAHHMYSMPPYPYLATDYGTQLSLFTHHNWIGGFCIVGAGAHAA
IFMVRDYDPTNNYNNLLDRVIRHRDAIISHLNWVCIFLGFHSFGLYIHND
TMSALGRPQDMFSDTAIQLQPVFAQWIQKTHFLAPQLTAPTALAATSATW
GGDVVAVGGKVAMMPISLGTSDFLVHHIHAFTIHVTVLILLKGVLFARSS
RLIPDKANLGFRFPCDGPGRGGTCQVSAWDHVFLGLFWMYNSLSIAIFHF
SWKMQSDVWGTVTASGVSHITGGNFAQSANTINGWLRDFLWAQSSQVIQS
YGSALSAYGLMFLGAHFVWAFSLMFLFSGRGYWQELIESIIWAHSKLKVA
PSIQPRALSITQGRAVGVAHYLLGGIATTWSFFLARIIAV

Ligand information

• Ligand ID: PQN
• InChI: InChI=1S/C31H46O2/c1-22(2)12-9-13-23(3)14-10-15-24(4)16-11-17-25(5)20-21-27-26(6)30(32)28-18-7-8-19-29(28)31(27)33/h7-8,18-20,22-24H,9-17,21H2,1-6H3/b25-20+/t23-,24-/m1/s1
• InChIKey: MBWXNTAXLNYFJB-NKFFZRIASA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC1=C(C(=O)c2ccccc2C1=O)CC=C(C)CCCC(C)CCCC(C)CCCC(C)C
  ACDLabs 10.04: O=C2c1c(cccc1)C(=O)C(=C2C)C\C=C(/C)CCCC(C)CCCC(C)CCCC(C)C
  OpenEye OEToolkits 1.5.0: CC1=C(C(=O)c2ccccc2C1=O)C\C=C(/C)\CCC[C@H](C)CCC[C@H](C)CCCC(C)C
  CACTVS 3.341: CC(C)CCC[CH](C)CCC[CH](C)CCCC(C)=CCC1=C(C)C(=O)c2ccccc2C1=O
  CACTVS 3.341: CC(C)CCC[C@@H](C)CCC[C@@H](C)CCCC(/C)=C/CC1=C(C)C(=O)c2ccccc2C1=O
• Formula: C31 H46 O2
• Name: PHYLLOQUINONE;
  VITAMIN K1;
  2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE
• ChEMBL: CHEMBL1550
• DrugBank: DB01022
• ZINC: ZINC000003831332
• PDB chain: 8cmo Chain A Residue 843

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cmo Cryo-EM structure of the Photosystem I - LHCI supercomplex from Coelastrella sp.
• Resolution: 2.81 Å
• Binding residue (original residue number in PDB): M684 F685 S688 G689 R690 W693 A717 L718
• Binding residue (residue number reindexed from 1): M674 F675 S678 G679 R680 W683 A707 L708
• Annotation score: 4

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sat Feb 22 04:45:03 2025

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 = '8cmo', asym_id = 'A', bs = 'BS42', title = 'Cryo-EM structure of the Photosystem I - LHCI supercomplex from Coelastrella sp.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='8cmo', asym_id='A', bs='BS42', title='Cryo-EM structure of the Photosystem I - LHCI supercomplex from Coelastrella sp.')

   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 = '0009579,0015979,0016020,0046872', uniprot = '', pdbid = '8cmo', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0009579,0015979,0016020,0046872', uniprot='', pdbid='8cmo', asym_id='A')

    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>