Structure of PDB 5znk Chain A

Receptor sequence

>5znkA (length=562) Species: 1280 (Staphylococcus aureus)

MKQSKVFIPTMRDVPSEAEAQSHRLLLKSGLIKQSTSGIYSYLPLATRVL
NNITAIVRQEMERIDSVEILMPALQQAELWEESGRWGAYGPELMRLQDRH
GRQFALGPTHEELVTSIVRNELKSYKQLPMTLFQIQSKFRDEKRPRFGLL
RGREFIMKDAYSFHADEASLDQTYQDMYQAYSRIFERVGINARPVVADSG
AIGGSHTHEFMALSAIGEDTIVYSKESDYTANIEKAEVVYEPNHKHSTVQ
PLEKIETPNVKTAQELADFLGRPVDEIAKTMIFKVDGEYIMVLVRGHHEI
NDIKLKSYFGTDNIELATQDEIVNLVSLGPVIDKEIKIYADNFVQDLNNL
VVGANEDGYHLINVNVGRDFNVDEYGDFRFILEGEKLSDGSGVAHFAEGI
EVGQVFKLGTKYSESMNATFLDNQGKAQPLIMGCYGIGISRTLSAIVEQN
HDDNGIVWPKSVTPFDLHLISINPKKDDQRELADALYAEFNTKFDVLYDD
RQERAGVKFNDADLIGLPLRIVVGKRASEGIVEVKERLTGDSEEVHIDDL
MTVITNKYDNLK

3D structure

• PDB: 5znk Structure-Guided Design of Halofuginone Derivatives as ATP-Aided Inhibitors Against Bacterial Prolyl-tRNA Synthetase.
• Chain: A
• Resolution: 2.07 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	ANP	A	R140 E142 R151 G152 F155 M157 E406 V407 G408 G443 R446	R140 E142 R151 G152 F155 M157 E401 V402 G403 G438 R441
BS02	MG	A	E406 Q409	E401 Q404
BS03	9G3	A	W80 R85 Y89 E92 L93 P108 T109 E111 R140 M157 Y161 F411 G441	W80 R85 Y89 E92 L93 P108 T109 E111 R140 M157 Y161 F406 G436

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sat Nov 30 10:15:38 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 = '5znk', asym_id = 'A', title = 'Structure-Guided Design of Halofuginone Derivati...ibitors Against Bacterial Prolyl-tRNA Synthetase.'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='5znk', asym_id='A', title='Structure-Guided Design of Halofuginone Derivati...ibitors Against Bacterial Prolyl-tRNA Synthetase.')

    839 

    840     if go:

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

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0000166,0002161,0004812,0004827,0005524,0005737,0006418,0006433', uniprot = '', pdbid = '5znk', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0000166,0002161,0004812,0004827,0005524,0005737,0006418,0006433', uniprot='', pdbid='5znk', 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>