Structure of PDB 3vdi Chain A Binding Site BS04

Receptor Information

>3vdi Chain A (length=356) Species: 34091 (Pelodictyon phaeum)

TTTAHSDYEIILEGGSSSWGQIKGRAKVNVPAALPLLPADCNIKIEAKPL
DAQKGVVRFTSQIESIVDSTKNKLVVEVDIANETKDRRIAVGEGEVSVGD
FSHKFSFEGSVVNMYYYRSDAVRRNVPNPVYMQGRQFHDIMMKVPLDNKD
LIETWEGFQQSISGGGVNFGDWIREFWFIGPAYTAINEGGQRISPIQVNN
FGVESGPVGVSRWKFSHAGSGIVDSISRWAELFPVEQLNKPASIEGGFRS
DSQGIEVKVDGNLPGVSRDAGGGLRRILNHPLIPLVHHGMVGKFNDFTVD
TQLKVVLPKGYKIRYAAPQFRSQNLEEYRWSGGAYARWVEHVCKGGTGQF
EVLYAQ

Ligand information

• Ligand ID: BCL
• InChI: InChI=1S/C55H75N4O6.Mg/c1-13-39-34(7)41-29-46-48(38(11)60)36(9)43(57-46)27-42-35(8)40(52(58-42)50-51(55(63)64-12)54(62)49-37(10)44(59-53(49)50)28-45(39)56-41)23-24-47(61)65-26-25-33(6)22-16-21-32(5)20-15-19-31(4)18-14-17-30(2)3;/h25,27-32,34-35,39-40,51H,13-24,26H2,1-12H3,(H-,56,57,58,59,60,62);/q-1;+2/p-1/b33-25+;/t31-,32-,34-,35+,39-,40+,51-;/m1./s1
• InChIKey: DSJXIQQMORJERS-AGGZHOMASA-M
• SMILES:
  OpenEye OEToolkits 2.0.7: CC[C@@H]1[C@H](C2=CC3=C(C(=C4[N-]3[Mg+2]56[N]2=C1C=C7[N-]5C8=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(=O)C)C
  CACTVS 3.385: [Mg++].CC[CH]1[CH](C)C2=Cc3[n-]c(C=C4N=C([CH](CCC(=O)OCC=C(C)CCC[CH](C)CCC[CH](C)CCCC(C)C)[CH]4C)C5=C6[N-]C(=CC1=N2)C(=C6C(=O)[CH]5C(=O)OC)C)c(C)c3C(C)=O
  CACTVS 3.385: [Mg++].CC[C@@H]1[C@@H](C)C2=Cc3[n-]c(C=C4N=C([C@@H](CCC(=O)OC\C=C(/C)CCC[C@H](C)CCC[C@H](C)CCCC(C)C)[C@@H]4C)C5=C6[N-]C(=CC1=N2)C(=C6C(=O)[C@@H]5C(=O)OC)C)c(C)c3C(C)=O
  OpenEye OEToolkits 2.0.7: CCC1C(C2=CC3=C(C(=C4[N-]3[Mg+2]56[N]2=C1C=C7[N-]5C8=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(=O)C)C
• Formula: C55 H74 Mg N4 O6
• Name: BACTERIOCHLOROPHYLL A
• DrugBank: DB01853
• PDB chain: 3vdi Chain A Residue 404

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3vdi Reinterpretation of the electron density at the site of the eighth bacteriochlorophyll in the FMO protein from Pelodictyon phaeum.
• Resolution: 1.99 Å
• Binding residue (original residue number in PDB): Y11 I13 G252 I283 L284 H286 P287 P290 H294 Y341 W344 C349 F356
• Binding residue (residue number reindexed from 1): Y8 I10 G246 I277 L278 H280 P281 P284 H288 Y335 W338 C343 F350
• Annotation score: 4

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Wed Dec 18 16:05:38 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 = '3vdi', asym_id = 'A', bs = 'BS04', title = 'Reinterpretation of the electron density at the ...phyll in the FMO protein from Pelodictyon phaeum.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='3vdi', asym_id='A', bs='BS04', title='Reinterpretation of the electron density at the ...phyll in the FMO protein from Pelodictyon phaeum.')

   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 = '0015979', uniprot = '', pdbid = '3vdi', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0015979', uniprot='', pdbid='3vdi', 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>