Structure of PDB 4ly3 Chain B Binding Site BS02

Receptor Information

>4ly3 Chain B (length=271) Species: 407148 (Campylobacter jejuni subsp. jejuni 81116)

GHMIKICIAGKNNIAVNSLQFILKNYFEADQIVVIPNKNDKGIDSWQKSL
LKFALDNNIKIVTLDEIYNIEQIIFFSLEFDQIIKIENFKSDRLFNIHFS
ALPKYKGVFTSITPILNNELESGVTLHRIDNGIDTGNIIDQHCFPIDIND
TARDLYFNYLKYGESIFKKNIQTIINNSYKDLKQTNINSSYFSRKDINLV
HKINFKKTSFEIHNQIRAFIFQEYQLPIINNSKIIKSILANEFIGYNVFE
EFENYFIISGIDGFKIIAQKL

Ligand information

• Ligand ID: 1YF
• InChI: InChI=1S/C17H27N3O15P2/c1-7-4-20(17(26)19-15(7)25)11-3-9(22)10(33-11)5-31-36(27,28)35-37(29,30)34-16-14(24)12(18-6-21)13(23)8(2)32-16/h4,6,8-14,16,22-24H,3,5H2,1-2H3,(H,18,21)(H,27,28)(H,29,30)(H,19,25,26)/t8-,9+,10-,11-,12+,13-,14-,16-/m1/s1
• InChIKey: XDTNOGIJZRWAPO-ADAYKIPUSA-N
• SMILES:
  ACDLabs 12.01: O=C1C(=CN(C(=O)N1)C2OC(C(O)C2)COP(=O)(OP(=O)(OC3OC(C(O)C(NC=O)C3O)C)O)O)C
  OpenEye OEToolkits 1.7.6: C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)NC=O)O
  CACTVS 3.385: C[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@@H](NC=O)[C@@H]1O
  OpenEye OEToolkits 1.7.6: CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)NC=O)O
  CACTVS 3.385: C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O)[CH](O)[CH](NC=O)[CH]1O
• Formula: C17 H27 N3 O15 P2
• Name: [(2R,3R,4S,5S,6R)-4-formamido-6-methyl-3,5-bis(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate
• ZINC: ZINC000098208061
• PDB chain: 4ly3 Chain B Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ly3 Structure of a sugar N-formyltransferase from Campylobacter jejuni.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): K9 E77 F78 H96 V106 F107 S109 D132 Y154 F219 Y222 Q223
• Binding residue (residue number reindexed from 1): K11 E79 F80 H98 V108 F109 S111 D134 Y156 F221 Y224 Q225
• Annotation score: 1

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Wed Dec 18 16:17:17 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 = '4ly3', asym_id = 'B', bs = 'BS02', title = 'Structure of a sugar N-formyltransferase from Campylobacter jejuni.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='4ly3', asym_id='B', bs='BS02', title='Structure of a sugar N-formyltransferase from Campylobacter jejuni.')

   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 = '0009058', uniprot = '', pdbid = '4ly3', asym_id = 'B'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0009058', uniprot='', pdbid='4ly3', 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>