Structure of PDB 5z66 Chain A Binding Site BS01

Receptor Information

>5z66 Chain A (length=512) Species: 550 (Enterobacter cloacae)

TQTTSPDILLGPLFNDVQSAKLFPDQKTFADAVPKSDPLMILADYRMQHT
QSSFDLRHFVEMNFTLPAEGEKYVPPAGQSLREHIDDLWPVLTRTTDKAS
NKWDSLLPLPKPYVVPGGRFREVYYWDSYFTMLGLAESDHWDKISDMVDN
FAYEIDTFGHIPNGNRSYYLSRSQPPFFSMMVELLATHDSDALKKYRPQM
EKEYAYWMDGVDALQPGQANKRVVKLDDGAILNRYWDDRDTPRPESWLDD
VNTAKSNPNRPATEIYRDLRSAAASGWDFSSRWMDDPQKLGTIRTTSIVP
VDLNALMFKMEKLLARASQESGDAASASKYEALATARQKAIESHLWNDKE
GWYADYDLKSKKVRNQLTAAALFPLYVKAAAQDRADKVAAATSSRLLKPG
GIATTTVNSGQQWDAPNGWAPLQWVAAEGLQNYGQEKVSMDVTWRFLKNV
QHTYDREKKLVEKYDVSTTGTGGGGGEYPLQDGFGWSNGVTLKMLDRVCP
KAKPCDSVPENQ

Ligand information

• Ligand ID: VDM
• InChI: InChI=1S/C14H25NO8/c16-3-5-1-7(11(20)13(22)9(5)18)15-8-2-6(4-17)10(19)14(23)12(8)21/h1,6-23H,2-4H2/t6-,7+,8+,9-,10-,11+,12+,13+,14+/m1/s1
• InChIKey: YCJYNBLLJHFIIW-MBABXGOBSA-N
• SMILES:
  CACTVS 3.341: OC[CH]1C[CH](N[CH]2C=C(CO)[CH](O)[CH](O)[CH]2O)[CH](O)[CH](O)[CH]1O
  ACDLabs 10.04: OC2C(NC1C=C(CO)C(O)C(O)C1O)CC(C(O)C2O)CO
  OpenEye OEToolkits 1.5.0: C1C(C(C(C(C1NC2C=C(C(C(C2O)O)O)CO)O)O)O)CO
  OpenEye OEToolkits 1.5.0: C1[C@@H]([C@H]([C@@H]([C@H]([C@H]1N[C@H]2C=C([C@H]([C@@H]([C@H]2O)O)O)CO)O)O)O)CO
  CACTVS 3.341: OC[C@H]1C[C@H](N[C@H]2C=C(CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@@H](O)[C@@H]1O
• Formula: C14 H25 N O8
• Name: (1S,2S,3R,6S)-4-(HYDROXYMETHYL)-6-{[(1S,2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-(HYDROXYMETHYL)CYCLOHEXYL]AMINO}CYCLOHEX-4-ENE-1,2,3-TRIOL;
  VALIDOXYLAMINE
• ChEMBL: CHEMBL1236649
• ZINC: ZINC000016052241
• PDB chain: 5z66 Chain A Residue 609

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5z66 Mechanistic insights into enzymatic catalysis by trehalase from the insect gut endosymbiont Enterobacter cloacae.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): P150 F154 Y158 W160 D161 N197 Y203 Q208 R277 E279 G310 D312 W447 E511 Y512 F518 W520
• Binding residue (residue number reindexed from 1): P116 F120 Y124 W126 D127 N163 Y169 Q174 R243 E245 G276 D278 W413 E477 Y478 F484 W486
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=6.69,Kd=206nM

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sat Nov 16 09:50:16 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 = '5z66', asym_id = 'A', bs = 'BS01', title = 'Mechanistic insights into enzymatic catalysis by...the insect gut endosymbiont Enterobacter cloacae.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='5z66', asym_id='A', bs='BS01', title='Mechanistic insights into enzymatic catalysis by...the insect gut endosymbiont Enterobacter cloacae.')

   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 = '0004555,0005975,0005991,0005993,0042597,0071474', uniprot = '', pdbid = '5z66', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0004555,0005975,0005991,0005993,0042597,0071474', uniprot='', pdbid='5z66', 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>