Structure of PDB 3odh Chain E

Receptor sequence

>3odhE (length=194) Species: 64972 (Oceanobacter kriegii)

MKIKRIEVLINNGSVPGIPMILNEIQDAIKTVSWPEGNNSFVINPVRKGN
GVKPIKNSCMRHLHQKGWALEHPVRIKAEMRPGPLDAVKMIGGKAFALEW
ETGNISSSHRAINKMVMGMLERVIIGGVLILPSRDMYNYLTDRVGNFREL
EPYFSVWRQFNLKDAYLAIVEIEHDSVDAQVSLIPKGTDGRAIR

3D structure

• PDB: 3odh Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI.
• Chain: E
• Resolution: 2.3 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	dna	E	N104 R143 T188 D189 G190	N104 R143 T188 D189 G190	PDBbind-CN: Kd=12.9nM
BS02	dna	E	V52 K56 G83 T102 R110 K114 T141 D142 R143 K186 G187 D189 G190 R191 A192	V52 K56 G83 T102 R110 K114 T141 D142 R143 K186 G187 D189 G190 R191 A192	PDBbind-CN: Kd=12.9nM
BS03	CA	E	D86 W100	D86 W100

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Tue Nov 26 05:52:20 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 = '3odh', asym_id = 'E', title = 'Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI.'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='3odh', asym_id='E', title='Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI.')

    839 

    840     if go:

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

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0000287,0003677,0009036,0009307', uniprot = '', pdbid = '3odh', asym_id = 'E'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0000287,0003677,0009036,0009307', uniprot='', pdbid='3odh', asym_id='E')

    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>