Structure of PDB 5vt3 Chain A Binding Site BS01

Receptor Information

>5vt3 Chain A (length=313) Species: 676 (Vibrio fluvialis)

KHSKLLILGSGPAGYTAAVYAARANLNPVLITGMQQGGQLTTTTEVENWP
GDPEGLTGPGLMDRMKEHAERFETEIIFDHINEVDFSTRPFVLKGDAASY
SCDALIISTGASAKYLGLESEEAFKGRGVSACATCDGFFYRNQKVAVVGG
GNTAVEEALYLSNIAAEVHLIHRRDSFRAEKILINRLMDKVQNGNIVLHT
DRVLDEVLGDEMGVTGVRLKDVKTGGTEELDVMGAFIAIGHSPNTQIFQG
QLDMKDGYILVKSGLEGNATQTSVEGIFAAGDVMDHNYRQAITSAGTGCM
AALDAERYLDSLN

Ligand information

• Ligand ID: NAP
• InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
• InChIKey: XJLXINKUBYWONI-NNYOXOHSSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
  CACTVS 3.341: NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
  CACTVS 3.341: NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
• Formula: C21 H28 N7 O17 P3
• Name: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
  2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
• ChEMBL: CHEMBL295069
• DrugBank: DB03461
• PDB chain: 5vt3 Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5vt3 High resolution structure of thioredoxin-disulfide reductase from Vibrio vulnificus CMCP6 in complex with NADP and FAD
• Resolution: 1.98 Å
• Binding residue (original residue number in PDB): L120 G154 G155 N156 T157 E160 H176 R177 R178 R182 I243 G244 H245 R293 Q294
• Binding residue (residue number reindexed from 1): L116 G150 G151 N152 T153 E156 H172 R173 R174 R178 I239 G240 H241 R289 Q290
• Annotation score: 4

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sat Apr 5 22:26:54 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 = '5vt3', asym_id = 'A', bs = 'BS01', title = 'High resolution structure of thioredoxin-disulfi...rio vulnificus CMCP6 in complex with NADP and FAD'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='5vt3', asym_id='A', bs='BS01', title='High resolution structure of thioredoxin-disulfi...rio vulnificus CMCP6 in complex with NADP and FAD')

   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 = '0004791,0005737,0016491,0019430', uniprot = '', pdbid = '5vt3', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0004791,0005737,0016491,0019430', uniprot='', pdbid='5vt3', 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>