Structure of PDB 6xio Chain A Binding Site BS01

Receptor Information

>6xio Chain A (length=462) Species: 2250255 (Methanosarcinales archaeon)

MDISEWEKRYNEAYSDISKSLKKVKGIFVAYNSNIDAIKHIYPRQIDSPA
DFVARLIISMRDGKAAEVPTYTTDIHEWLTDNLGFDEARMGGQAGIISNL
LANMGIKNVIAYVPWLSKEQAEYFVDSENLLHPVVENGKLELKHPKEAYN
PDNKPKVNWIIEFSKGLEVKFAIVVPRDNRLIVSSRPPWIRIDMSEELYE
HLPEIGKNIDGAILSGYQMIKEEYEDGKTYKDYVEKAVNVIKRLKEGNPD
IRIHVEFTSIQNKLIRKAILKDIVRKHVHSLGLDTVEVANALNVLGYEEL
AYSVIKKDENAIVALYEGAVILLHELKLERVHVHSLGYYICVVSKDSPVS
PEDHRKSLLFASTVAAARALLGNINSLDDIEAGLDVPVSEQGYNQLEKLE
KYLVRRGICTLEDFENGCICTPNHDVIIIPTKVVEKPVATVGIGDTISAA
AFVSVLAKMKKK

Ligand information

• Ligand ID: AT4
• InChI: InChI=1S/C10H15N5O9P2S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(23-10)1-22-25(18,19)24-26(20,21)27/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H2,11,12,13)(H2,20,21,27)/t4-,6-,7-,10-/m1/s1
• InChIKey: HCIKUKNAJRJFOW-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)O[P@@](=O)(O)S)O)O)N
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)S)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(S)=O)[C@@H](O)[C@H]3O
  ACDLabs 10.04: O=P(O)(S)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(S)=O)[CH](O)[CH]3O
• Formula: C10 H15 N5 O9 P2 S
• Name: 5'-O-[(R)-HYDROXY(THIOPHOSPHONOOXY)PHOSPHORYL]ADENOSINE;
  ADENOSINE 5'-O-(2-THIODIPHOSPHATE)
• ChEMBL: CHEMBL335206
• PDB chain: 6xio Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6xio Structure of an ancestral ADP-dependent kinase with fructose-6P reveals key residues for binding, catalysis, and ligand-induced conformational changes.
• Resolution: 3.12 Å
• Binding residue (original residue number in PDB): R206 H360 S361 V459 V460 G468 I469 G470 D471 I473
• Binding residue (residue number reindexed from 1): R180 H334 S335 V433 V434 G442 I443 G444 D445 I447
• Annotation score: 1

Gene Ontology

--> -->

UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Feb 21 21:38:51 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 = '6xio', asym_id = 'A', bs = 'BS01', title = 'Structure of an ancestral ADP-dependent kinase w...ysis, and ligand-induced conformational changes. '

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='6xio', asym_id='A', bs='BS01', title='Structure of an ancestral ADP-dependent kinase w...ysis, and ligand-induced conformational changes. ')

   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 = '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>