Structure of PDB 6nhz Chain A

Receptor sequence

>6nhzA (length=303) Species: 1773 (Mycobacterium tuberculosis)

SMFEFDNLAPMLATHGTVAGLKASQWAFEGMWDGYRLLVEADHGAVRLRS
RSGRDVTAEYPQLRALAEDLADHHVVLDGEAVVLDSSGVPSFSQMQNRGR
DTRVEFWAFDLLYLDGRALLGTRYQDRRKLLETLANATSLTVPELLPGDG
AQAFACSRKHGWEGVIAKRRDSRYQPGRRCASWVKDKHWNTQEVVIGGWR
AGGVGSLLMGIPGPGGLQFAGRVGTGLSERELANLKEMLAPLHTDESPFD
VPLPARDAKGITYVKPALVAEVRYSEWTPEGRLRQSSWRGLRPDKKPSEV
VRE

3D structure

• PDB: 6nhz Structures of ATP-bound DNA ligase D in a closed domain conformation reveal a network of amino acid and metal contacts to the ATP phosphates.
• Chain: A
• Resolution: 1.8 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	ATP	A	H465 E479 M481 W482 R501 E530 F559 I616 K618 R629 K635 K637	H15 E29 M31 W32 R51 E80 F109 I166 K168 R179 K185 K187

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sat Nov 16 05:46:51 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>()

   1443                 pubmed=display_regular_ligand(pdbid,asym_id,lig3,ligIdx,title)

   1444         else:

=> 1445             pubmed,uniprot=display_protein_receptor(pdbid,asym_id,title)

   1446     

   1447     uniprot_line=''

pubmed = '', uniprot = '', display_protein_receptor = <function display_protein_receptor>, pdbid = '6nhz', asym_id = 'A', title = 'Structures of ATP-bound DNA ligase D in a closed...o acid and metal contacts to the ATP phosphates. '

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='6nhz', asym_id='A', title='Structures of ATP-bound DNA ligase D in a closed...o acid and metal contacts to the ATP phosphates. ')

    839 

    840     if go:

=>  841         display_go(go,uniprot,pdbid,asym_id)

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0003910,0005524,0006281,0006310', uniprot = '', pdbid = '6nhz', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003910,0005524,0006281,0006310', uniprot='', pdbid='6nhz', 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>