Structure of PDB 5j63 Chain A Binding Site BS01

Receptor Information

>5j63 Chain A (length=302) Species: 656414 (Escherichia coli H736)

MKTVVFAYHDMGCLGIEALLAAGYEISAIFTHTDNPGEKAFYGSVARLAA
ERGIPVYAPDNVNHPLWVERIAQLSPDVIFSFYYRHLIYDEILQLAPAGA
FNLHGSLLPKYRGRAPLNWVLVNGETETGVTLHRMVKRADAGAIVAQLRI
AIAPDDIAITLHHKLCHAARQLLEQTLPAIKHGNILEIAQRENEATCFGR
RTPDDSFLEWHKPASVLHNMVRAVADPWPGAFSYVGNQKFTVWSSRVHPK
AQPGSVISVAPLLIACGDGALEIVTGQAGDGITMQGSQLAQTLGLVQGSR
LN

Ligand information

• Ligand ID: G3N
• InChI: InChI=1S/C14H23N3O15P2/c15-5-3-28-13(11(22)8(5)19)31-34(26,27)32-33(24,25)29-4-6-9(20)10(21)12(30-6)17-2-1-7(18)16-14(17)23/h1-2,5-6,8-13,19-22H,3-4,15H2,(H,24,25)(H,26,27)(H,16,18,23)/t5-,6+,8-,9+,10+,11+,12+,13+/m0/s1
• InChIKey: GWBAKYBSWHQNMQ-IAZOVDBXSA-N
• SMILES:
  ACDLabs 12.01: OP(OP(OCC1C(O)C(C(O1)N2C(NC(C=C2)=O)=O)O)(O)=O)(=O)OC3C(C(C(CO3)N)O)O
  OpenEye OEToolkits 2.0.4: C1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)O)O)N
  CACTVS 3.385: N[C@H]1CO[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](O)[C@H]1O
  OpenEye OEToolkits 2.0.4: C1[C@@H]([C@@H]([C@H]([C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)O)O)N
  CACTVS 3.385: N[CH]1CO[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](O)[CH]1O
• Formula: C14 H23 N3 O15 P2
• Name: (2R,3R,4S,5S)-5-amino-3,4-dihydroxytetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate
• ZINC: ZINC000030730249
• PDB chain: 5j63 Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5j63 Structure of the Escherichia coli ArnA N-formyltransferase domain in complex with N(5) -formyltetrahydrofolate and UDP-Ara4N.
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): E38 Y83 R85 H104 R114 A115 N118 R201 T202 P203 V224
• Binding residue (residue number reindexed from 1): E38 Y83 R85 H104 R114 A115 N118 R201 T202 P203 V224
• Annotation score: 1

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sat Nov 16 10:19:04 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 = '5j63', asym_id = 'A', bs = 'BS01', title = 'Structure of the Escherichia coli ArnA N-formylt... with N(5) -formyltetrahydrofolate and UDP-Ara4N.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='5j63', asym_id='A', bs='BS01', title='Structure of the Escherichia coli ArnA N-formylt... with N(5) -formyltetrahydrofolate and UDP-Ara4N.')

   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 = '0003824,0009058', uniprot = '', pdbid = '5j63', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003824,0009058', uniprot='', pdbid='5j63', 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>