Structure of PDB 4mdt Chain D

Receptor sequence

>4mdtD (length=293) Species: 562 (Escherichia coli)

QRTLKRIVQATGVGLHTGKKVTLTLRPAPANTGVIYRRTDLNPPVDFPAD
AKSVRDTMLCTCLVNEHDVRISTVEHLNAALAGLGIDNIVIEVNAPEIPI
MDGSAAPFVYLLLDAGIDELNSAKKFVRIKETVRVEDGDKWAEFKPYNGF
SLDFTIDFNHPAIDSSNQRYAMNFSADAFMRQISRARTFGFMRDIEYLQS
RGLCLGGSFDCAIVVDDYRVLNEDGLRFEDEFVRHKMLDAIGDLFMCGHN
IIGAFTAYKSGHALNNKLLQAVLAKQEAWEYVTFQDDAELPLA

3D structure

• PDB: 4mdt Structure of the Bacterial Deacetylase LpxC Bound to the Nucleotide Reaction Product Reveals Mechanisms of Oxyanion Stabilization and Proton Transfer.
• Chain: D
• Resolution: 2.59 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	ZN	D	H79 H238 D242	H76 H235 D239
BS02	24G	D	L18 K143 I159 D160 F161 F192 F194 M195 I198 G210 S211 A215 K239 K262 G264 H265	L15 K140 I156 D157 F158 F189 F191 M192 I195 G207 S208 A212 K236 K259 G261 H262

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Mon Feb 17 05:06:00 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>()

   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 = '4mdt', asym_id = 'D', title = 'Structure of the Bacterial Deacetylase LpxC Boun...s of Oxyanion Stabilization and Proton Transfer. '

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='4mdt', asym_id='D', title='Structure of the Bacterial Deacetylase LpxC Boun...s of Oxyanion Stabilization and Proton Transfer. ')

    839 

    840     if go:

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

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0008759,0009245', uniprot = '', pdbid = '4mdt', asym_id = 'D'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0008759,0009245', uniprot='', pdbid='4mdt', 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>