Structure of PDB 4yd9 Chain Z

Receptor sequence

>4yd9Z (length=825) Species: 6637 (Todarodes pacificus)

VRGNLVRKNVDRLSLQEINSLIHALKRMQKDRSSDGFETIASFHALPPLC
PNPTAKHRHACCLHGMATFPQWHRLYVVQFEHSLNRHGAIVGVPYWDWTY
PMTEVPGLLTSEKYTDPFTGIETFNPFNHGHISFISPETMTTREVSEHLF
EQPALGKQTWLFNNIILALEQTDYCDFEVQFEIVHNSIHSWLGGKELYSL
NHLHYAAYDPAFFLHHSNVDRLWVVWQELQKFRGLPAYESNCAIELMSQP
LKPFSFGAPYNLNPVTTKYSKPSDVFNYKQNFHYEYDMLEMNGMSIAQLE
SYIRQERQKDRVFAGFLLEGFGSSAYATFQVCPDVGDCYEGSHFSVLGGS
TEMPWAFDRLYKMEITDILQAMALKFDSHFTIKTKIVAHNGTELPESLLP
EATIVRIPPSAQNLEVAIPLNRIRRNINSLESRDVQNLMSALKRLKEDES
DFGFQTIAGYHGSLMCPTPEAPEYACCLHGMPTFMHWHRVYLLHFEESMR
RHGASVAVPYWDWTMPSDNLPSLLGDADYYDAWTDSVIENPFLRGHIKYE
DTYTVREIQPELFALAEGQKESTLFKDVMLMFEQEDYCDFEVQAEVIHNS
IHYLIGGHQKYAMSSLMFSSFDPIFYVHHSMVDRLWAIWQELQKHRKLPH
DKAYCALDQMAFPMKPFIWESNPNPTTRAVSTPSKLFDYKSLGYDYDHLN
FHGMSIGQLEALIQKQKKADRVFAGFLLHGIKISADVHLKICIEADCQEA
GVIFVLGGETEMPWHFDRNYKMDITDVLKKRNIPPEALFEHDSKIRLEVE
IKSVDGAVLDPNSLPKPSLIYAPAK

3D structure

• PDB: 4yd9 Crystal Structure of the 3.8-MDa Respiratory Supermolecule Hemocyanin at 3.0 angstrom Resolution
• Chain: Z
• Resolution: 3.0 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	CUO	Z	H2126 H2146 H2155 H2267 H2271 H2298	H44 H64 H73 H185 H189 H216
BS02	CUO	Z	H2543 H2561 H2570 H2680 H2684 F2707 H2711	H461 H479 H488 H598 H602 F625 H629

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Mon Apr 28 04:35:12 2025

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>()

   1443                 pubmed=display_regular_ligand(pdbid,asym_id,lig3,ligIdx,title)

   1444         else:

=> 1445             pubmed,uniprot=display_protein_receptor(pdbid,asym_id,title)

   1446     

   1447     uniprot_line=''

pubmed = '', uniprot = '', display_protein_receptor = <function display_protein_receptor>, pdbid = '4yd9', asym_id = 'Z', title = 'Crystal Structure of the 3.8-MDa Respiratory Supermolecule Hemocyanin at 3.0 angstrom Resolution'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='4yd9', asym_id='Z', title='Crystal Structure of the 3.8-MDa Respiratory Supermolecule Hemocyanin at 3.0 angstrom Resolution')

    839 

    840     if go:

=>  841         display_go(go,uniprot,pdbid,asym_id)

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0016491', uniprot = '', pdbid = '4yd9', asym_id = 'Z'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0016491', uniprot='', pdbid='4yd9', asym_id='Z')

    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>