Structure of PDB 7cm9 Chain B Binding Site BS01

Receptor Information

>7cm9 Chain B (length=693) Species: 56811 (Psychrobacter sp.)

AMKKENLKILAKKAQTIAIVGANYRFATRVLLENLDKMDFTGTIYLVNPR
YENIDGVRCYQSLLEIEDTIDVVVGLVNPQLMIQVASNASKINAKVLVIP
GGGYGESGVEGQNIQNAILERAADSGMRIVGPNCMGYLNMHAQFTPYIGT
LHRPLRPIKKGPVSIISQSGSVNDAFIASKLGISKIYSTGNEADVQMHDY
LNLLAEDPETSVIILYIEAIRNHLSFLRALDLCSKNKKPVIAIKVGRTIK
SAAVANAHSGALAGDYEIEKLFLEGHGVLFVEDIDQAVAVALLLSQPYLP
TVNTVAALTVSGGQAGILLDLAEDYGVDFPDFSAVTNYEIASKLPELGGL
SNPLDIWGKSSKDFSEVSNICLSSIVKDADIGIITVAIDAPIGQGDHEFD
FTSIPAKDLASLRGNSDKPFLYFSHIQTEFDPRVESILDEAGIAVIQGSR
NALVACRALFKYKEFLEKNNHTPIYSVEDLSIQKGLKLLHDNEGRKLLDE
SGFVSPREQVVTSLQEGVDYAESIGYPVVLKAQGLAHKTDVGGVALNIKS
AAKLKKAWGKMEHLNSPYYLIQEMVTDGFETILAYRTDMNYGPVVIFGLG
GIYTELFNEVVLAVPPITHKKAEQMVKSIPMLWKSIEGYRGNPALDLEAL
TASIVQMGETAMEKYEEIVEFEINPLSVRVKGVVALDVLASVK

Ligand information

• Ligand ID: ATP
• InChI: InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: ZKHQWZAMYRWXGA-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  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)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
• Formula: C10 H16 N5 O13 P3
• Name: ADENOSINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL14249
• DrugBank: DB00171
• ZINC: ZINC000004261765
• PDB chain: 7cm9 Chain B Residue 801

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7cm9 A novel ATP dependent dimethylsulfoniopropionate lyase in bacteria that releases dimethyl sulfide and acryloyl-CoA.
• Resolution: 2.249 Å
• Binding residue (original residue number in PDB): H292 V563 K565 H571 K572 T573 L580 Q606 M608 V609 E614 N708 P709 L720 D721
• Binding residue (residue number reindexed from 1): H258 V529 K531 H537 K538 T539 L546 Q572 M574 V575 E580 N674 P675 L686 D687
• Annotation score: 4

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sat Nov 16 04:16:58 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 = '7cm9', asym_id = 'B', bs = 'BS01', title = 'A novel ATP dependent dimethylsulfoniopropionate... that releases dimethyl sulfide and acryloyl-CoA.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='7cm9', asym_id='B', bs='BS01', title='A novel ATP dependent dimethylsulfoniopropionate... that releases dimethyl sulfide and acryloyl-CoA.')

   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 = '0005524,0046872', uniprot = '', pdbid = '7cm9', asym_id = 'B'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0005524,0046872', uniprot='', pdbid='7cm9', asym_id='B')

    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>