Structure of PDB 6xio Chain A

Receptor sequence

>6xioA (length=462) Species: 2250255 (Methanosarcinales archaeon)

MDISEWEKRYNEAYSDISKSLKKVKGIFVAYNSNIDAIKHIYPRQIDSPA
DFVARLIISMRDGKAAEVPTYTTDIHEWLTDNLGFDEARMGGQAGIISNL
LANMGIKNVIAYVPWLSKEQAEYFVDSENLLHPVVENGKLELKHPKEAYN
PDNKPKVNWIIEFSKGLEVKFAIVVPRDNRLIVSSRPPWIRIDMSEELYE
HLPEIGKNIDGAILSGYQMIKEEYEDGKTYKDYVEKAVNVIKRLKEGNPD
IRIHVEFTSIQNKLIRKAILKDIVRKHVHSLGLDTVEVANALNVLGYEEL
AYSVIKKDENAIVALYEGAVILLHELKLERVHVHSLGYYICVVSKDSPVS
PEDHRKSLLFASTVAAARALLGNINSLDDIEAGLDVPVSEQGYNQLEKLE
KYLVRRGICTLEDFENGCICTPNHDVIIIPTKVVEKPVATVGIGDTISAA
AFVSVLAKMKKK

3D structure

• PDB: 6xio Structure of an ancestral ADP-dependent kinase with fructose-6P reveals key residues for binding, catalysis, and ligand-induced conformational changes.
• Chain: A
• Resolution: 3.12 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	AT4	A	R206 H360 S361 V459 V460 G468 I469 G470 D471 I473	R180 H334 S335 V433 V434 G442 I443 G444 D445 I447
BS02	F6P	A	D36 E90 G114 G115 Q116 K179 S210 M245	D36 E67 G91 G92 Q93 K156 S184 M219

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Thu Feb 20 06:43:16 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 = '6xio', asym_id = 'A', title = 'Structure of an ancestral ADP-dependent kinase w...ysis, and ligand-induced conformational changes. '

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='6xio', asym_id='A', title='Structure of an ancestral ADP-dependent kinase w...ysis, and ligand-induced conformational changes. ')

    839 

    840     if go:

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

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0000287,0005737,0005975,0006000,0006096,0008443,0016773', uniprot = '', pdbid = '6xio', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0000287,0005737,0005975,0006000,0006096,0008443,0016773', uniprot='', pdbid='6xio', 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>