Structure of PDB 2xti Chain A Binding Site BS01

Receptor Information

>2xti Chain A (length=433) Species: 6279 (Brugia malayi)

TGVKIRDLVKHRNERVCIKGWIHRMRRQGKSLMFFILRDGTGFLQVLLMD
KLCQTYDALTVNTECTVEIYGAIKEVEAPNGHELIADFWKIIGNAPPGGI
DNVLNEEASVDKMLDNRHLVIRGENAAALLRLRAAATRAMREHFYNAGYV
EVAPPTLVQTQVEGGSTLFNLDYFGEQSFLTQSSQLYLETCIPTLGDVFC
IAQSYRAEKSRTRRHLAEYAHVEAECPFITLDDLMEKIEELVCDTVDRLL
ADEEAKKLLEHINPKFQPPERPFLRMEYKDAIKWLQEHNVENEFGNTFTY
GEDIAEAAERFMTDTINKPILLNRFPSEIKAFYMQRDAKDNTLTESVDLL
MPGVGEIVGGSMRIWKFDELSKAFKNVEIDPKPYYWYLDQRLYGTCPHGG
YGLGLERFICWLTNTNHIRDVCLYPRFVGRCVP

Ligand information

• Ligand ID: NB8
• InChI: InChI=1S/C14H20N7O10P/c15-5(1-7(22)20-26)14(25)31-32(27,28)29-2-6-9(23)10(24)13(30-6)21-4-19-8-11(16)17-3-18-12(8)21/h3-6,9-10,13,23-24,26H,1-2,15H2,(H,20,22)(H,27,28)(H2,16,17,18)/t5-,6+,9+,10+,13+/m0/s1
• InChIKey: LNQDDLRGTAFRLA-VWJPMABRSA-N
• SMILES:
  OpenEye OEToolkits 1.6.1: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)OC(=O)[C@H](CC(=O)NO)N)O)O)N
  OpenEye OEToolkits 1.6.1: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OC(=O)C(CC(=O)NO)N)O)O)N
  ACDLabs 10.04: O=C(NO)CC(N)C(=O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.352: N[CH](CC(=O)NO)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
  CACTVS 3.352: N[C@@H](CC(=O)NO)C(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
• Formula: C14 H20 N7 O10 P
• Name: 5'-O-[(R)-{[(2S)-2-amino-4-(hydroxyamino)-4-oxobutanoyl]oxy}(hydroxy)phosphoryl]adenosine
• ZINC: ZINC000058650246
• PDB chain: 2xti Chain A Residue 1549

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2xti A Hybrid Structural Model of the Complete Brugia Malayi Cytoplasmic Asparaginyl-tRNA Synthetase.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): E278 S298 Q300 R321 E323 H330 L331 Y334 H336 E338 Y448 E471 I472 V473 G474 R478 Y516 G517 G519 R522
• Binding residue (residue number reindexed from 1): E163 S183 Q185 R206 E208 H215 L216 Y219 H221 E223 Y333 E356 I357 V358 G359 R363 Y401 G402 G404 R407
• Annotation score: 3

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Nov 15 23:54:43 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 = '2xti', asym_id = 'A', bs = 'BS01', title = 'A Hybrid Structural Model of the Complete Brugia Malayi Cytoplasmic Asparaginyl-tRNA Synthetase.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='2xti', asym_id='A', bs='BS01', title='A Hybrid Structural Model of the Complete Brugia Malayi Cytoplasmic Asparaginyl-tRNA Synthetase.')

   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 = '0000166,0003676,0004812,0004816,0005524,0006418,0006421', uniprot = '', pdbid = '2xti', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0000166,0003676,0004812,0004816,0005524,0006418,0006421', uniprot='', pdbid='2xti', 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>