Structure of PDB 3vqy Chain A Binding Site BS01

Receptor Information
>3vqy Chain A (length=257) Species: 2209 (Methanosarcina mazei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PALTKSQTDRLEVLLNPKDESGKPFRELESELLSRRKKDLQQIYAEEREN
YLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQIFRV
DKNFCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKESDGKEHLEE
FTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGGDTLDVMHGDLEL
SSAVVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSGSYY
NGISTNL
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain3vqy Chain A Residue 501 [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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PDB3vqy A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site
Resolution2.4 Å
Binding residue
(original residue number in PDB)		R330 E332 H338 L339 F342 M344 E396 L397 S399 G423 R426
Binding residue
(residue number reindexed from 1)		R139 E141 H147 L148 F151 M153 E199 L200 S202 G226 R229
Annotation score4
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Sat Nov 16 16:22:13 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 = '3vqy', asym_id = 'A', bs = 'BS01', title = 'A novel crystal form of pyrrolysyl-tRNA syntheta... and an asparagine residue in the catalytic site '
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='3vqy', asym_id='A', bs='BS01', title='A novel crystal form of pyrrolysyl-tRNA syntheta... and an asparagine residue in the catalytic site ')
   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 = '0000049,0004812,0005524,0043039', uniprot = '', pdbid = '3vqy', asym_id = 'A'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0000049,0004812,0005524,0043039', uniprot='', pdbid='3vqy', 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>