Structure of PDB 5t61 Chain M Binding Site BS03

Receptor Information
>5t61 Chain M (length=568) Species: 145261 (Methanothermobacter wolfeii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EYIIKNGFVYCPLNGVDGEKMDICVKDGKIVESVSDSAKVIDASGKIVMP
GGVDPHSHIAGAKVNVGRMYRPEDSKRDAEKFKGGRAGSGFSVPSTFMTG
YRYAQMGYTTAMEAAMPPLLARHTHEEFHDTPIIDHAAYPLFGNNWFVME
YLKEGDVDACAAYASWLLRATKGYTIKIVNPAGTEAWGWGGNVHGIYDPA
PYFDITPAEIIKGLAEVNEKLQLPHSIHLHCNDLGHPGNYETTLASFDVP
KNIKPNPATGSRDTVLYATHVQFHSYGGTTWRDFVSEAPKIADYVNKNDH
IVIDVGQITLDETTTMTADGPMEYDLHSLNGLKWANCDVELETGSGVVPF
IYSARAPVPAVQWAIGMELFLLIDNPEKVCLTTDSPNAGPFTRYPRVIAW
LMSNKYRMNLIEGELHKWAQRKSTVATIDREYTFSEIAQITRATSAKVLG
LSDTKGHLGVGADADIAVYDINPETVDPSAEYMAIEEAFSRAACVLKDGE
IVVKDGEVVASPHGRTYWVDTQVDESIYSEVLANVESKFKQYYSVNFANY
PVQDDYLPKSAPVKGVML
Ligand information
Ligand IDMFN
InChIInChI=1S/C35H44N4O16/c40-19-36-16-23-15-21(18-55-23)17-54-22-3-1-20(2-4-22)13-14-37-28(41)10-7-26(34(50)51)39-30(43)11-8-27(35(52)53)38-29(42)9-5-24(32(46)47)25(33(48)49)6-12-31(44)45/h1-4,15,18-19,24-27H,5-14,16-17H2,(H,36,40)(H,37,41)(H,38,42)(H,39,43)(H,44,45)(H,46,47)(H,48,49)(H,50,51)(H,52,53)/t24?,25?,26-,27+/m1/s1
InChIKeyRGBIJPWAWLXPOC-XRVZLLLRSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C(CCC(=O)O)C(C(=O)O)CCC(=O)NC(C(=O)O)CCC(=O)NC(C(=O)O)CCC(=O)NCCc2ccc(OCc1cc(oc1)CNC=O)cc2
OpenEye OEToolkits 1.5.0c1cc(ccc1CCNC(=O)CCC(C(=O)O)NC(=O)CCC(C(=O)O)NC(=O)CCC(C(CCC(=O)O)C(=O)O)C(=O)O)OCc2cc(oc2)CNC=O
OpenEye OEToolkits 1.5.0c1cc(ccc1CCNC(=O)CC[C@H](C(=O)O)NC(=O)CC[C@@H](C(=O)O)NC(=O)CC[C@H]([C@H](CCC(=O)O)C(=O)O)C(=O)O)OCc2cc(oc2)CNC=O
CACTVS 3.341OC(=O)CCC([CH](CCC(=O)N[CH](CCC(=O)N[CH](CCC(=O)NCCc1ccc(OCc2coc(CNC=O)c2)cc1)C(O)=O)C(O)=O)C(O)=O)C(O)=O
CACTVS 3.341OC(=O)CCC([C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@H](CCC(=O)NCCc1ccc(OCc2coc(CNC=O)c2)cc1)C(O)=O)C(O)=O)C(O)=O)C(O)=O
FormulaC35 H44 N4 O16
NameN-[4,5,7-TRICARBOXYHEPTANOYL]-L-GAMMA-GLUTAMYL-N-{2-[4-({5-[(FORMYLAMINO)METHYL]-3-FURYL}METHOXY)PHENYL]ETHYL}-D-GLUTAMINE
ChEMBL
DrugBank
ZINC
PDB chain5t61 Chain M Residue 603 [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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PDB5t61 The methanogenic CO2 reducing-and-fixing enzyme is bifunctional and contains 46 [4Fe-4S] clusters.
Resolution2.55 Å
Binding residue
(original residue number in PDB)		H231 H271 F274 W282 R283 T316 M323 L327 L330 F351 Y353 V359 D385 N388 H417
Binding residue
(residue number reindexed from 1)		H230 H270 F273 W281 R282 T315 M322 L326 L329 F350 Y352 V358 D384 N387 H416
Annotation score1
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Tue Dec 3 06:42:23 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 = '5t61', asym_id = 'M', bs = 'BS03', title = 'The methanogenic CO2 reducing-and-fixing enzyme is bifunctional and contains 46 [4Fe-4S] clusters.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='5t61', asym_id='M', bs='BS03', title='The methanogenic CO2 reducing-and-fixing enzyme is bifunctional and contains 46 [4Fe-4S] clusters.')
   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 = '0016810', uniprot = '', pdbid = '5t61', asym_id = 'M'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0016810', uniprot='', pdbid='5t61', asym_id='M')
    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>