Structure of PDB 6t6v Chain A Binding Site BS02

Receptor Information

>6t6v Chain A (length=742) Species: 85698 (Achromobacter xylosoxidans)

GPYRRLWFTLIAVLAVTFALLGFYGGEVYRQAPPIPEEVASADGTRLFGR
DDILDGQTAWQSIGGMQLGSIWGHGAYQAPDWTADWLHRELMAWLDLAAR
DAHGRDYGQLDAPAQAALREQLKAEYRANRADAAGGKLTLSPRRAQAVAQ
TEAYYDQLFSDAPALHRSRENYAMKENTLPDANRRRQMTHFFFWTAWAAG
TEREGTSVTYTNNWPHEPLIGNHPSSENVMWSIISVVVLLAGIGLLIWAW
AFLRGKEEDEPPAPARDPLTTFALTPSQRALGKYLFLVVALFGFQVLLGG
FTAHYTVEGQKFYGIDLSQWFPYSLVRTWHIQSALFWIATGFLAAGLFLA
PLINGGRDPKYQKAGVDILFWALVLVVVGSFAGNYLAIAQIMPPDLNFWL
GHQGYEYVDLGRLWQIGKFAGICFWLVLMLRGIVPALRTPGGDKNLLALL
TASVGAIGLFYGAGFFYGERTHLTVMEYWRWWIVHLWVEGFFAVFATTAL
AFIFSTLGLVSRRMATTASLASASLFMLGGIPGTFHHLYFAGTTTPVMAV
GASFSALEVVPLIVLGHEAWENWRLKTRAPWMENLKWPLMCFVAVAFWNM
LGAGVFGFMINPPVSLYYIQGLNTTPVHAHAALFGVYGFLALGFTLLVLR
YIRPQYALSPGLMKLAFWGLNLGLALMIFTSLLPIGLIQFHASVSEGMWY
ARSEAFMQQDILKTLRWGRTFGDVVFLLGALAMVVQVILGLL

Ligand information

• Ligand ID: HEM
• 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,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
• InChIKey: KABFMIBPWCXCRK-RGGAHWMASA-L
• SMILES:
  OpenEye OEToolkits 1.7.6: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
  CACTVS 3.385: CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5|6|N2=C1C=c7n5c(=CC8=N|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C
  ACDLabs 12.01: C=1c3c(c(c4C=C5C(=C(C=6C=C7C(=C(C8=CC=2C(=C(C=1N=2[Fe](n34)(N5=6)N78)CCC(=O)O)C)\C=C)C)\C=C)C)C)CCC(=O)O
• Formula: C34 H32 Fe N4 O4
• Name: PROTOPORPHYRIN IX CONTAINING FE;
  HEME
• DrugBank: DB18267
• PDB chain: 6t6v Chain A Residue 802

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6t6v The active form of quinol-dependent nitric oxide reductase fromNeisseria meningitidisis a dimer.
• Resolution: 4.5 Å
• Binding residue (original residue number in PDB): E407 Y408 W482 V489 V560 T626 H629 A630 Y638
• Binding residue (residue number reindexed from 1): E406 Y407 W481 V488 V559 T625 H628 A629 Y637
• Annotation score: 1

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Wed Dec 4 07:41:13 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 = '6t6v', asym_id = 'A', bs = 'BS02', title = 'The active form of quinol-dependent nitric oxide reductase fromNeisseria meningitidisis a dimer.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='6t6v', asym_id='A', bs='BS02', title='The active form of quinol-dependent nitric oxide reductase fromNeisseria meningitidisis a dimer.')

   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 = '0004129,0009060,0016020,0020037', uniprot = '', pdbid = '6t6v', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0004129,0009060,0016020,0020037', uniprot='', pdbid='6t6v', 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>