Structure of PDB 3vqy Chain A Binding Site BS02

Receptor Information
>3vqy Chain A (length=257) Species: 2209 (Methanosarcina mazei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PALTKSQTDRLEVLLNPKDESGKPFRELESELLSRRKKDLQQIYAEEREN
YLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQIFRV
DKNFCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKESDGKEHLEE
FTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGGDTLDVMHGDLEL
SSAVVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSGSYY
NGISTNL
Ligand information
Ligand IDLBY
InChIInChI=1S/C11H22N2O4/c1-11(2,3)17-10(16)13-7-5-4-6-8(12)9(14)15/h8H,4-7,12H2,1-3H3,(H,13,16)(H,14,15)/t8-/m0/s1
InChIKeyVVQIIIAZJXTLRE-QMMMGPOBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(C)(C)OC(=O)NCCCCC(C(=O)O)N
OpenEye OEToolkits 1.7.6CC(C)(C)OC(=O)NCCCC[C@@H](C(=O)O)N
CACTVS 3.370CC(C)(C)OC(=O)NCCCC[CH](N)C(O)=O
ACDLabs 12.01O=C(OC(C)(C)C)NCCCCC(C(=O)O)N
CACTVS 3.370CC(C)(C)OC(=O)NCCCC[C@H](N)C(O)=O
FormulaC11 H22 N2 O4
NameN~6~-(tert-butoxycarbonyl)-L-lysine
ChEMBL
DrugBank
ZINCZINC000002384792
PDB chain3vqy Chain A Residue 502 [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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PDB3vqy A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site
Resolution2.4 Å
Binding residue
(original residue number in PDB)		Y306 N346 S399 W417 A420 G421
Binding residue
(residue number reindexed from 1)		Y115 N155 S202 W220 A223 G224
Annotation score1
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Sat Nov 16 12:42:10 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 = '3vqy', asym_id = 'A', bs = 'BS02', title = 'A novel crystal form of pyrrolysyl-tRNA syntheta... and an asparagine residue in the catalytic site '
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='3vqy', asym_id='A', bs='BS02', title='A novel crystal form of pyrrolysyl-tRNA syntheta... and an asparagine residue in the catalytic site ')
   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 = '0000049,0004812,0005524,0043039', uniprot = '', pdbid = '3vqy', asym_id = 'A'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0000049,0004812,0005524,0043039', uniprot='', pdbid='3vqy', 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>