Structure of PDB 4gw9 Chain B Binding Site BS01

Receptor Information

>4gw9 Chain B (length=621) Species: 258594 (Rhodopseudomonas palustris CGA009)

GSPAFGTADLSNCEREEIHLAGSIQPHGALLVVSEPDHRIIQASANAAEF
LNLGSVLGVPLAEIDGDLLIKILPHLDPTAEGMPVAVRCRIGNPSTEYDG
LMHRPPEGGLIIELERAGPPIDLSGTLAPALERIRTAGSLRALCDDTALL
FQQCTGYDRVMVYRFDEQGHGEVFSERHVPGLESYFGNRYPSSDIPQMAR
RLYERQRVRVLVDVSYQPVPLEPRLSPLTGRDLDMSGCFLRSMSPIHLQY
LKNMGVRATLVVSLVVGGKLWGLVACHHYLPRFIHFELRAICELLAEAIA
TRITALESFAQSQSELFVQRLEQRMIEAITREGDWRAAIFDTSQSILQPL
HADGCALVYEDQIRTIGDVPSTQDVREIAGWLDRQPRAAVTSTASLGLDV
PELAHLTRMASGVVAAPISDHRGEFLMWFRPERVHTVTWGGDPKDTPADL
SPRRSFAKWHQVVEGTSDPWTAADLAAARTIGQTVADIVLQFRAVRTLIA
REQYEQFSSQVHASMQPVLITDAEGRILLMNDSFRDMLPAGSPSAVHLDD
LAGFFVESNDFLRNVAELIDHGRGWRGEVLLRGAGNRPLPLAVRADPVTR
TEDQSLGFVLIFSDATDRRTA

Ligand information

• Ligand ID: BLA
• InChI: InChI=1S/C33H34N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h7-8,13-15,34H,1-2,9-12H2,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b26-13-,27-14-,29-15-
• InChIKey: GWZYPXHJIZCRAJ-SRVCBVSDSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: Cc1c(c([nH]c1\C=C/2\C(=C(C(=O)N2)C=C)C)\C=C/3\C(=C(C(=N3)\C=C/4\C(=C(C(=O)N4)C)C=C)C)CCC(=O)O)CCC(=O)O
  OpenEye OEToolkits 1.5.0: Cc1c(c([nH]c1C=C2C(=C(C(=O)N2)C=C)C)C=C3C(=C(C(=N3)C=C4C(=C(C(=O)N4)C)C=C)C)CCC(=O)O)CCC(=O)O
  CACTVS 3.341: Cc1c([nH]c(C=C2N=C(C=C3NC(=O)C(=C3C=C)C)C(=C2CCC(O)=O)C)c1CCC(O)=O)C=C4NC(=O)C(=C4C)C=C
  CACTVS 3.341: Cc1c([nH]c(\C=C2/N=C(\C=C3/NC(=O)C(=C3C=C)C)C(=C2CCC(O)=O)C)c1CCC(O)=O)\C=C4/NC(=O)C(=C4C)C=C
• Formula: C33 H34 N4 O6
• Name: BILIVERDINE IX ALPHA
• ZINC: ZINC000103534374
• PDB chain: 4gw9 Chain B Residue 900

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4gw9 Structure of a bacteriophytochrome and light-stimulated protomer swapping with a gene repressor.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): C20 M168 Y170 D201 I202 P203 Y210 R216 M250 I253 H254 Y257 M261 V268 H284 S468
• Binding residue (residue number reindexed from 1): C13 M161 Y163 D194 I195 P196 Y203 R209 M243 I246 H247 Y250 M254 V261 H277 S455
• Annotation score: 4

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Thu Feb 20 04:12:53 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 = '4gw9', asym_id = 'B', bs = 'BS01', title = 'Structure of a bacteriophytochrome and light-stimulated protomer swapping with a gene repressor.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='4gw9', asym_id='B', bs='BS01', title='Structure of a bacteriophytochrome and light-stimulated protomer swapping with a gene repressor.')

   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 = '0006355,0009584', uniprot = '', pdbid = '4gw9', asym_id = 'B'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0006355,0009584', uniprot='', pdbid='4gw9', asym_id='B')

    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>