Structure of PDB 5ld1 Chain D Binding Site BS03

Receptor Information
>5ld1 Chain D (length=261) Species: 277 (Meiothermus ruber) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKKYRVQPDGRFELKRFDPDDTSAFEGGKQAALEALAVLNRRLEKLQELL
YAEGQHKVLVVLQAMDAGGKDGTIRVVFDGVNPSGVRVASFGVPTEQELA
RDYLWRVHQQVPRKGELVIFNRSHYEDVLVVRVKNLVPQQVWQKRYRHIR
EFERMLADEGTTILKFFLHISKDEQRQRLQERLDNPEKRWKFRMGDLEDR
RLWDRYQEAYEAAIRETSTEYAPWYVIPANKNWYRNWLVSHILVETLEGL
AMQYPQPIVIE
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain5ld1 Chain D Residue 1002 [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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PDB5ld1 Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures.
Resolution2.09 Å
Binding residue
(original residue number in PDB)		D66 A67 G68 G69 K70 D71 R122 R182 W190 K191
Binding residue
(residue number reindexed from 1)		D66 A67 G68 G69 K70 D71 R122 R182 W190 K191
Annotation score5
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Sat Nov 16 03:47:53 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 = '5ld1', asym_id = 'D', bs = 'BS03', title = 'Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='5ld1', asym_id='D', bs='BS03', title='Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures.')
   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 = '0006797,0008976,0016776', uniprot = '', pdbid = '5ld1', asym_id = 'D'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0006797,0008976,0016776', uniprot='', pdbid='5ld1', asym_id='D')
    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>