Structure of PDB 6rn4 Chain D Binding Site BS04

Receptor Information

>6rn4 Chain D (length=684) Species: 1280998 (Escherichia coli HVH 50 (4-2593475))

QALKKYTIDLTERAEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEP
GVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEER
LKGVLNDLAKQEGNVILFIDALHTMVGAGMDAGNMLKPALARGELHCVGA
TTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTIAILRGLKERYELHHHV
QITDPAIVAAATLSHRYIADRQLPDKAIDLIDEAASSIRMQIDSPEELDR
LDRRIIQLKLEQQALMLDMLNEELSDKERQYSELEEEWKAEKASLSGTQT
IKAELEQAKIAIEQARRVGDLARMSELQYGKIPELEKQLEAATQLEGKTM
RLLRNKVTDAEIAEVLARWTGIPVSRMMESEREKLLRMEQELHHRVIGQN
EAVDAVSNAIRRSRAGLADPNRPIGSFLFLGPTGVGKTELCKALANFMFD
SDEAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEGGYLTEAVRRRPYSVI
LLDAVEKAHPDVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNLGSDL
IQERFGELDYAHMKELVLGVVSHNFRPEFINRIDEVVVFHPLGEQHIASI
AQIQLKRLYKRLEERGYEIHISDEALKLLSENGYDPVYGARPLKRAIQQQ
IENPLAQQILSGELVPGKVIRLEVNEDRIVAVQH

Ligand information

• Ligand ID: AGS
• InChI: InChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
• InChIKey: NLTUCYMLOPLUHL-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
  CACTVS 3.370: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
  CACTVS 3.370: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
  ACDLabs 12.01: O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
• Formula: C10 H16 N5 O12 P3 S
• Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER;
  ATP-GAMMA-S;
  ADENOSINE 5'-(3-THIOTRIPHOSPHATE);
  ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);
  ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
• ChEMBL: CHEMBL131890
• DrugBank: DB02930
• ZINC: ZINC000008295128
• PDB chain: 6rn4 Chain E Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6rn4 Two-Step Activation Mechanism of the ClpB Disaggregase for Sequential Substrate Threading by the Main ATPase Motor.
• Resolution: 4.2 Å
• Binding residue (original residue number in PDB): R331 R332
• Binding residue (residue number reindexed from 1): R168 R169
• Annotation score: 4

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Thu Dec 5 10:43:45 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 = '6rn4', asym_id = 'D', bs = 'BS04', title = 'Two-Step Activation Mechanism of the ClpB Disagg...ial Substrate Threading by the Main ATPase Motor.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='6rn4', asym_id='D', bs='BS04', title='Two-Step Activation Mechanism of the ClpB Disagg...ial Substrate Threading by the Main ATPase Motor.')

   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 = '0005524,0005737,0009408,0016887,0042026', uniprot = '', pdbid = '6rn4', asym_id = 'D'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0005524,0005737,0009408,0016887,0042026', uniprot='', pdbid='6rn4', 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>