Structure of PDB 8vdw Chain B Binding Site BS04

Receptor Information
>8vdw Chain B (length=332) Species: 29466 (Veillonella parvula) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QPSQVGTYEKILTIANRIMNGGEITKEEAIELIHTSDDDTMILLAMADKI
RQHFNDNSVDVCAIVNARSGKCPENCKFCAQSAHHNTGVQEYPFMDEESI
LQAARKAKEAGAIRFSIVTSGRNTNNPDEFDQIIHVLGRIKNEIGLEICC
SLGLLTYEQALKLKEVGVTRYHSNIETAPSHFPDICTTHSYEDKMFTIDN
AQKAGIRVCSGGILGLNETLEQRVEMAFELKRLHIDSVPLNILNPVKGTP
FESNEALRPLDILRTFAVFRFILPNALIRTAGGREVNLRDLQAYALKGGL
NGIMVGGYLTTGGRSPQDDLQMIQDLELTRNT
Ligand information
Ligand IDSAM
InChIInChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
InChIKeyMEFKEPWMEQBLKI-FCKMPRQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
ACDLabs 10.04[O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H22 N6 O5 S
NameS-ADENOSYLMETHIONINE
ChEMBLCHEMBL1235831
DrugBank
ZINC
PDB chain8vdw Chain B Residue 404 [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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PDB8vdw X-Ray Crystal Structure of the biotin synthase from V. parvula
Resolution1.807 Å
Binding residue
(original residue number in PDB)		F85 T126 S158 G160 N181 E183 I220 L250 N251
Binding residue
(residue number reindexed from 1)		F78 T119 S151 G153 N174 E176 I213 L243 N244
Annotation score5
Enzymatic activity
Enzyme Commision number 2.8.1.6: biotin synthase.
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Sat Nov 30 07:23:32 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 = '8vdw', asym_id = 'B', bs = 'BS04', title = 'X-Ray Crystal Structure of the biotin synthase from V. parvula'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='8vdw', asym_id='B', bs='BS04', title='X-Ray Crystal Structure of the biotin synthase from V. parvula')
   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 = '0003824,0004076,0009102,0051536', uniprot = '', pdbid = '8vdw', asym_id = 'B'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003824,0004076,0009102,0051536', uniprot='', pdbid='8vdw', 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>