Structure of PDB 6gdr Chain A Binding Site BS04

Receptor Information
>6gdr Chain A (length=256) Species: 314275 (Alteromonas mediterranea) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVDGLQLAKQYGHQDINIAEYWVSEKLDGIRARWDGTELRTRNNNKIDAP
AWFTANWPKATIDGELWIARGQFERTASIVLSKLTLPSKRWAKVRFMAFD
MPVAGQSFDSRLNMLNNLKEATPNPTFAVVSQFTLSSVNALEEKLEQVTL
SGGEGLMLHHKKAFYHSGRSDKLIKVKQFEDAEAKVLAHFAGKGKFKGMM
GSLLVETPAGVQFKLGTGFSEKERRAPPAVGSWVTFKFYGVTKNGKPRFA
SFLRVR
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain6gdr Chain D Residue 300 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6gdr DNA binding with a minimal scaffold: structure-function analysis of Lig E DNA ligases.
Resolution2.33 Å
Binding residue
(original residue number in PDB)		K34 L35 R39 R50 E73 M191 K209
Binding residue
(residue number reindexed from 1)		K26 L27 R31 R42 E65 M157 K175
Annotation score4
Gene Ontology
--> -->
 
 
UnboundLocalError		Python 3.6.8: /usr/bin/python3
Sun Dec 1 19:11:56 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 = '6gdr', asym_id = 'A', bs = 'BS04', title = 'DNA binding with a minimal scaffold: structure-function analysis of Lig E DNA ligases.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='6gdr', asym_id='A', bs='BS04', title='DNA binding with a minimal scaffold: structure-function analysis of Lig E DNA ligases.')
   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 = '0003910,0005524,0006281,0006310', uniprot = '', pdbid = '6gdr', asym_id = 'A'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003910,0005524,0006281,0006310', uniprot='', pdbid='6gdr', 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>