Structure of PDB 5m7p Chain A Binding Site BS02

Receptor Information

>5m7p Chain A (length=441) Species: 641140 (Brucella abortus str. 2308 A)

MAADILVVDDEVDIRDLVAGILSDEGHETRTAFDADSALAAINDRAPRLV
FLDIWLQGSRLDGLALLDEIKKQHPELPVVMISGHGNIETAVSAIRRGAY
DFIEKPFKADRLILVAERALETSKLKREVSDLRLVGTSLAMNQLRQTIER
VAPTNSRIMITGPSGAGKELVARAIHAQSSRANGPFVTVNAATITPERME
IELFGTEMDKVGALEEAHGGILYLDEVADMPRETQNKILRVLVDQQFERV
GGTKRVKVDVRIISSTAQNLEGMIAEGTFREDLFHRLSVVPVQVPALAAR
REDIPSLVEFFMKQIAEQAGIKPRKIGPDAMAVLQAHSWPGNLRQLRNNV
ERLMILTRGDDPDELVTADLLPAEIGDTLPRAPTESDQHIMALPLREARE
RFEKEYLIAQINRFGGNISRTAEFVGMERSALHRKLKSLGV

Ligand information

• Ligand ID: ADP
• InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 5m7p Chain A Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5m7p Three-Dimensional Structure of Full-Length NtrX, an Unusual Member of the NtrC Family of Response Regulators.
• Resolution: 2.36 Å
• Binding residue (original residue number in PDB): L142 V143 G173 G175 K176 E177 L178 L355 R356
• Binding residue (residue number reindexed from 1): L134 V135 G165 G167 K168 E169 L170 L343 R344
• Annotation score: 5
• Binding affinity: MOAD: Kd=70uM

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Mon Feb 17 21:01:38 2025

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 = '5m7p', asym_id = 'A', bs = 'BS02', title = 'Three-Dimensional Structure of Full-Length NtrX,...Member of the NtrC Family of Response Regulators.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='5m7p', asym_id='A', bs='BS02', title='Three-Dimensional Structure of Full-Length NtrX,...Member of the NtrC Family of Response Regulators.')

   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 = '0000160,0005524,0006355,0008134,0016887,0043565', uniprot = '', pdbid = '5m7p', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0000160,0005524,0006355,0008134,0016887,0043565', uniprot='', pdbid='5m7p', 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>