Structure of PDB 4yd9 Chain S

Receptor sequence

>4yd9S (length=1656) Species: 6637 (Todarodes pacificus)

NLIRKNVDTLTPDEILNLQVSLRAMQDDEGASGYQAISAYHGEPADCKAA
DGSTIVCCLHGMPTFPMWHRLYLVQFEQALVAHGSTLGIPYWDWTKPMTQ
LPELVQHPLFIDPTGKKAKKNVFYSGEIKFENKVTARAVDARLYQASQEG
QKNFLLEGVLNALEQEDFCHFEVQLEVAHNPIHYLVGGRFTHSMSSLEYT
SYDPLFFLHHSNVERHFALWQALQKHRGLPTRPNCGLNLFHSPMEPFGRD
TNPFAITKDNSKASSLFDYEHLGYAFDDLSLNGMTIEELEALLKQRRSGA
RAFANFRLGGIKTSANVRIKLCIPTEDKRQSDNCDNDAGQFFILGGTNEM
PWNFAFPYLHEITDTVLSLGLALDSNYYVTAEVTAINGTLMPTQTIPRPI
VTYIPPQGFKDVNMVNMDTSSLRFRKDISSLTTEEEYELRVAMERFMSDK
SINGYQALAEFHGLPAKCPRPDALNRVACCIHGMATFPHWHRLVVMQFEN
ALFTRGSPIGVPYWDWTKPFTALPSLLADETYVDPYTKETKPNPFFKAPI
EFLKAGVHTSRQIDERLFKQPSKGDHGFLYDGLSLAFEQDDFCDFEVQFE
VTHNSIHAWTGGSEPYSMSSLHYTSFDPMFWLHHSQVDRLWAIWQALQIQ
RGKPYKTYCANSEVYRPMKPFAFKSPLNNDEKTREHSVPTDVYDYQAELA
YTYDTLFFGGLSIRELQRYVEEAKSKDRVFAGFLLMGIQTSANVDLFVVA
GGNEFFVGSIAVLGGSKEMTWRFDRVYKHEITDALGALGVDMFAEYTLRV
DIKDVNGTALPPTAIPPPIVIFVPGIADANVKFDEQHRSRKNVDSMTVSE
MNALRTAMAAFAADKEVTGYQQVAAFHGSTQWCPSPDAAQKYACCHHGMA
TFPHWHRLIALNFENGLRRNGWSGGLPYWDWTRPIDALPALVLEAEYTDA
NGEAKPNPFFSGAIDSIGASTSRAPTEALYEKPDFGKYTHLANEIISALE
QEDFCDFEVQYEIAHNHIHALVGGTEAVSMASLEYSAFDPIFMLHHSNVD
RIWATWQALQKFRGKAYNSANCAIEILRKPMSPFSLASDINPDAMTREYS
VPFDVFNYKKNFHYEYDTLELNGLSIAQLSREINRRKAKNRVAVTFMLEG
LKKSLLVEYFIAADGTDQKMKAGEFYVLGSENEMPWKFDRPYKSDITYVM
DAMKLHYTDKYHVELRITDMTGAEVTDLKLVTSVIYEPGIGNFGEGRRWI
SPITSASRIRKNLLDFEDGEMESLRNAFKQMADEGRYEEIASFHGVPAQC
PSEDGTMVHTCCLHGMPVFPHWHRLYVSLVEDELLARGSGVAVPYWDWVE
PFDELPRLINEATFYNSRTLQIEPNPFFKGKISFENAETDRDTQPELFGN
RYLYDHTLFVFEQTDFCEFEVHYEVLHNTIHSWLGGRDVHSMSSLDYAAY
DPVFFLHHSNVDRLWAIWQELQRYRKLSYNEANCALPLMNQPMRPFSNST
ANNDRLTFTNSRPNDVFDYQNVLHYKYDTLNFAGLSIPQLERILQKNQGR
DRIFAGFLLHGIKASADVRIYICVPTGIGEENCGNYAGIFSVLGGETEMP
WQFDRLFRYEITDELKKLGLNQNSHFRVEMELTAVNGSKITQKIFPNPTI
IFVPSD

3D structure

• PDB: 4yd9 Crystal Structure of the 3.8-MDa Respiratory Supermolecule Hemocyanin at 3.0 angstrom Resolution
• Chain: S
• 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	S	H41 H60 H69 H179 H183 H210	H41 H60 H69 H179 H183 H210
BS02	CUO	S	H462 H482 H491 H603 H607 H634	H462 H482 H491 H603 H607 H634
BS03	CUO	S	H877 H897 H906 H1015 H1019 F1042 H1046	H877 H897 H906 H1015 H1019 F1042 H1046
BS04	CUO	S	H1294 H1314 H1323 H1427 H1431 F1454 H1458	H1294 H1314 H1323 H1427 H1431 F1454 H1458

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sat Nov 16 07:37:49 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>()

   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 = 'S', 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='S', 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 = 'S'

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

    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>