Structure of PDB 6yk9 Chain A Binding Site BS01

Receptor Information

>6yk9 Chain A (length=341) Species: 694436 (Methanolacinia paynteri G-2000)

TIKKVAILGAGCYRTHSATGITNFARACEVAEMVGKPEIAMTHSTIAMAA
ELKYLAGIDNIVISDPSFAGEFTVVKDFDYNEVIKAHKENPETIMPKIRE
KVNELAKTVPKPPKGAIHFVHPEDLGLKVTTDDREAVRDADLIITWLPKG
DMQKGIIEKFAGDIKQGAIITHACTIPTTLFYKIFEELGIADKVEVTSYH
PGAVPEMKGQVYIAEGYASEEAINTIYELGKKARGHAFKLPAELIGPVCD
MCAALTAITYAGLLVYRDAVMNILGAPAGFSQMMATESLEQITAYMKKVG
IKNLEENLDPGVFLGTADSMNFGPIAEILPTVLKSLEKRAK

Ligand information

• Ligand ID: FEG
• InChI: InChI=1S/C19H23N6O11P/c1-6-8(3-10(26)27)22-16(30)7(2)14(6)36-37(32,33)34-4-9-12(28)13(29)18(35-9)25-5-21-11-15(25)23-19(20)24-17(11)31/h5,9,12-13,18,28-29H,3-4H2,1-2H3,(H,22,30)(H,26,27)(H,32,33)(H3,20,23,24,31)/t9-,12-,13-,18-/m1/s1
• InChIKey: GTHOTKPHMGEHFD-ACDAHVMNSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: Cc1c(nc(c(c1O[P@@](=O)(O)OCC2[C@H]([C@H](C(O2)n3cnc4c3N=C(NC4=O)N)O)O)C)O)CC(=O)O
  ACDLabs 10.04: O=C(O)Cc4nc(O)c(c(OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O)c4C)C
  CACTVS 3.341: Cc1c(O)nc(CC(O)=O)c(C)c1O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4C(=O)NC(=Nc34)N
  CACTVS 3.341: Cc1c(O)nc(CC(O)=O)c(C)c1O[P@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC(=Nc34)N
  OpenEye OEToolkits 1.5.0: Cc1c(nc(c(c1OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3N=C(NC4=O)N)O)O)C)O)CC(=O)O
• Formula: C19 H23 N6 O11 P
• Name: 5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine
• ZINC: ZINC000058650286
• PDB chain: 6yk9 Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6yk9 The Hydride Transfer Process in NADP-dependent Methylene-tetrahydromethanopterin Dehydrogenase.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): G12 S65 D66 P67 P113 P114 D134 W147 L148 P149 K150 I157 T176
• Binding residue (residue number reindexed from 1): G11 S64 D65 P66 P112 P113 D133 W146 L147 P148 K149 I156 T175
• Annotation score: 1

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Mon Nov 25 09:29:55 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>()

   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 = '6yk9', asym_id = 'A', bs = 'BS01', title = 'The Hydride Transfer Process in NADP-dependent Methylene-tetrahydromethanopterin Dehydrogenase.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='6yk9', asym_id='A', bs='BS01', title='The Hydride Transfer Process in NADP-dependent Methylene-tetrahydromethanopterin Dehydrogenase.')

   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 = '0019386,0047068', uniprot = '', pdbid = '6yk9', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0019386,0047068', uniprot='', pdbid='6yk9', 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>