Structure of PDB 8rv0 Chain Y Binding Site BS08

Receptor Information

>8rv0 Chain Y (length=495) Species: 2916410 (Trichlorobacter ammonificans)

GRETCYACHTEVKSLKENSKHAAIACTVCHDKTKEHLEKGPDVKPVTKID
QAVCGSCHKNQYESFYAVHHDPTGARKEKGIPAGRSPLQDKLLAGHGFTF
EHAEPRGHAYMVVDQFAVDRFQGGRYQFKGGWKNYDKVGKTWDILEDRGP
NAKLPETAMAGNPTCIQCKSSDLILQWKHLGEKGGKFDRTSNVNDVVKAI
NNPVGCIHCHDPHGAQPRIVRDGLIAAIEKDPAKNIFAKNGKTDLKVIDF
RGFRKIGVMEKTDSRMMCAQCHVEYNCNPGTQRTDGKPVTFADARTNHFP
LKNSLQLLEHYRSIDFFDFKHAVTGAKLIKFQHPEAETYAGSAHDKAGVQ
CHQCHMPQVKGKDGKKYSTHGVVKPIQMVQESCISCHKDYTPNKAKFMIE
TIRNYTKGKMRKSEYWLAQLIDTFAVAQREGVSPTILDQARLKHEEAHAL
WEYWTAENSDGFHNPEQARQSLTGSISASKAGVKLLNDAIMAVKQ

Ligand information

• Ligand ID: HEC
• InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,9-12H2,1-6H3,(H,39,40)(H,41,42);/q-4;+4/b21-7?,22-8?,26-13-,29-14-,30-15-,31-16-;
• InChIKey: HXQIYSLZKNYNMH-LJNAALQVSA-N
• SMILES:
  ACDLabs 10.04: O=C(O)CCC1=C(C2=CC6=C(C(=C/C)\C5=CC4=C(C(\C3=Cc7c(c(c8C=C1N2[Fe](N34)(N56)n78)CCC(=O)O)C)=C/C)C)C)C
  OpenEye OEToolkits 1.5.0: CC=C1C(=C2C=C3C(=CC)C(=C4N3[Fe]56N2C1=Cc7n5c(c(c7C)CCC(=O)O)C=C8N6C(=C4)C(=C8CCC(=O)O)C)C)C
  CACTVS 3.341: C\C=C1/C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)\C7=C/C)C=C1N2[Fe@@]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
  CACTVS 3.341: CC=C1C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)C7=CC)C=C1N2[Fe]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
• Formula: C34 H34 Fe N4 O4
• Name: HEME C
• PDB chain: 8rv0 Chain Y Residue 608

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8rv0 Crystal structure of octaheme nitrite reductase from Trichlorobacter ammonificans in complex with nitrite
• Resolution: 1.55 Å
• Binding residue (original residue number in PDB): A380 H381 S419 C420 C423 H424 Y427 M435 P502
• Binding residue (residue number reindexed from 1): A343 H344 S382 C383 C386 H387 Y390 M398 P465
• Annotation score: 1

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Mon Nov 25 11:18:31 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 = '8rv0', asym_id = 'Y', bs = 'BS08', title = 'Crystal structure of octaheme nitrite reductase ...chlorobacter ammonificans in complex with nitrite'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='8rv0', asym_id='Y', bs='BS08', title='Crystal structure of octaheme nitrite reductase ...chlorobacter ammonificans in complex with nitrite')

   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 = '0042279,0042597', uniprot = '', pdbid = '8rv0', asym_id = 'Y'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0042279,0042597', uniprot='', pdbid='8rv0', asym_id='Y')

    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>