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BioLiP

Structure of PDB 6lm0 Chain B Binding Site BS01

Receptor Information
>6lm0 Chain B (length=227) Species: 1954171 (Calothrix sp. NIES-2098) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSGMTQFWLWVGFIGMVIGCIYFGMKASAMRRREGMEFPLESFFITLWAA
ALYLTMILGETVTPINGQTVFWGRYIDWVVTTPLLLMELGVIAGLRPKLI
AGVMGADIFMIVTGFIGAVEAPPYNYLWWLISTGSFLAILGSLLTEYSAS
AKRRNGRINSLFQTLRNILIVLWICYPIVWILGAEGFHVISVGWETLCYS
VLDVCAKVGFGFVVVSAGNETLAQASN
Ligand information
Ligand IDRET
InChIInChI=1S/C20H28O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6,8-9,11-13,15H,7,10,14H2,1-5H3/b9-6+,12-11+,16-8+,17-13+
InChIKeyNCYCYZXNIZJOKI-OVSJKPMPSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC(=C\C=O)/C=C/C=C(C)/C=C/C1=C(C)CCCC1(C)C
ACDLabs 12.01O=C\C=C(\C=C\C=C(\C=C\C1=C(C)CCCC1(C)C)C)C
OpenEye OEToolkits 1.7.0CC1=C(C(CCC1)(C)C)/C=C/C(=C/C=C/C(=C/C=O)/C)/C
OpenEye OEToolkits 1.7.0CC1=C(C(CCC1)(C)C)C=CC(=CC=CC(=CC=O)C)C
CACTVS 3.370CC(=CC=O)C=CC=C(C)C=CC1=C(C)CCCC1(C)C
FormulaC20 H28 O
NameRETINAL
ChEMBLCHEMBL81379
DrugBank
ZINCZINC000004228262
PDB chain6lm0 Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6lm0 A unique clade of light-driven proton-pumping rhodopsins evolved in the cyanobacterial lineage.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		W75 T79 M107 W126 S129 F133 W170 Y173 P174 W177 D200 K204
Binding residue
(residue number reindexed from 1)		W78 T82 M110 W129 S132 F136 W173 Y176 P177 W180 D203 K207
Annotation score4
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Wed May 21 22:27:24 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>()
   1701     title=pdb2title(pdbid)
   1702     if bs.startswith("BS"):
=> 1703         pubmed,uniprot=display_interaction(pdbid,asym_id,bs,title)
   1704     else:
   1705         if lig3:
pubmed = '', uniprot = '', display_interaction = <function display_interaction>, pdbid = '6lm0', asym_id = 'B', bs = 'BS01', title = 'A unique clade of light-driven proton-pumping rhodopsins evolved in the cyanobacterial lineage.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='6lm0', asym_id='B', bs='BS01', title='A unique clade of light-driven proton-pumping rhodopsins evolved in the cyanobacterial lineage.')
   1326         display_ec(ec,csaOrig,csaRenu)
   1327     if go:
=> 1328         display_go(go,uniprot,pdbid,asym_id)
   1329     return pubmed,uniprot
   1330 
global display_go = <function display_go>, go = '0005216,0006811,0016020', uniprot = '', pdbid = '6lm0', asym_id = 'B'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0005216,0006811,0016020', uniprot='', pdbid='6lm0', asym_id='B')
    484         '''.replace("$namespace_link",namespace_link
    485           ).replace("$namespace",namespace
=>  486           ).replace("$uniprot",u
    487         ))
    488         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>