Structure of PDB 6yrd Chain E Binding Site BS01

Receptor Information
>6yrd Chain E (length=305) Species: 1200984 (Streptomyces lividans 1326) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PEPQMVLSPLTSAAIFLVVTIDSGGEDTVRDLLSDVASLERAVGFRAQPD
GRLSCVTGIGSEAWDRLFSGARPAGLHPFRELDGPVHRAVATPGDLLFHI
RASRLDLCFALATEIMGRLRGAVTPQDEVHGFKYFDERDMLGFVDGTENP
TGAAARRAVLVGAEDPAFAGGSYAVVQKYLHDIDAWEGLSVEAQERVIGR
RKMTDVELSDDVKPADSHVALTSVTGPDGSDLEILRDNMPFGSVGREEFG
TYFIGYARTPEVTETMLERMFLGTASAPHDRILDFSTAVTGSLFFTPAAD
FLEDL
Ligand information
Ligand IDHEM
InChIInChI=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-;
InChIKeyKABFMIBPWCXCRK-RGGAHWMASA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c2n3c(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 3.385CC1=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 12.01C=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
FormulaC34 H32 Fe N4 O4
NamePROTOPORPHYRIN IX CONTAINING FE;
HEME
ChEMBL
DrugBankDB18267
ZINC
PDB chain6yrd Chain E Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6yrd Serial Femtosecond Zero Dose Crystallography Captures a Water-Free Distal Heme Site in a Dye-Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in Fe IV =O Formation.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		D146 V151 D152 G153 T154 E155 Y186 R207 H225 T229 R243 F260 M273 L274 M277 I289
Binding residue
(residue number reindexed from 1)		D139 V144 D145 G146 T147 E148 Y179 R200 H218 T222 R236 F253 M266 L267 M270 I282
Annotation score4
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Thu Nov 28 00:38:16 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 = '6yrd', asym_id = 'E', bs = 'BS01', title = 'Serial Femtosecond Zero Dose Crystallography Cap...ytic Role for an Arginine in Fe IV =O Formation. '
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='6yrd', asym_id='E', bs='BS01', title='Serial Femtosecond Zero Dose Crystallography Cap...ytic Role for an Arginine in Fe IV =O Formation. ')
   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 = '0004601,0020037', uniprot = '', pdbid = '6yrd', asym_id = 'E'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0004601,0020037', uniprot='', pdbid='6yrd', asym_id='E')
    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>