Structure of PDB 3u4a Chain B Binding Site BS03

Receptor Information

>3u4a Chain B (length=742) Species: 702656 (compost metagenome)

KMNQFINALMAKMTLDEKIGQLNLPGAGDITTGQASSSGIAQKIKEGKVG
GLFNIKSVTKIKEVQRIAVEESRLKIPLLFGMDVIHGYETAFPIPLGLSC
TWDMELIEKSARIAAIEASADGICWTFSPMVDISRDPRWGRVSEGSGEDP
YLGAQIAKAMVKGYQGKDFSDNTSIMACVKHFALYGAGEAGRDYNTVDMS
RVRMYNEYFPPYKAAVDAGVGSVMTSFNEIDGIPATGNKWLMTDVLRKRI
GAFKGFVVTNYTAINEMIDHGMGDLQTVSALALRAGVDMDMVGEGFLTTL
KKSLQEGKITQAQIDAACKRILEAKYKLGLFSDPYKYCNEERARTQIFTP
EHRKIAREIAAQSFVLLKNDNNVLPLKKSGTIALVGPLADNRVNMPGTWS
VAAKHAESVSLLEGLKKAAGNDARILYAHGSNLDEDKSLIERATMFGKTL
KYDPRPKDVVIKEAVDIANQADVIVAALGESAEMSGEASSRSNIEIPALQ
RELLQALLKTGKPVVLVLFTGRPLALTWEHENVPAILNVWFAGTEAGDAI
SDALFGVVNPSGKLSATFPRNVGQVPIYYNHKNTGRPLPEGQWFQKFRSN
YLDVPNDPLYPFGYGLSFTKFTYGDLKLSSTNLKGNQTLTASIELTNSGD
YDGAEVVQLYIRDLVGSTTRPVKELKGFQKVFLKKGETKTITFKITPEDL
KFYNYDLKYDWEPGEFVIMVGGNSRDLKSQKINWLKDPAFLY

Ligand information

• Ligand ID: BGC
• InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6-/m1/s1
• InChIKey: WQZGKKKJIJFFOK-VFUOTHLCSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: C(C1C(C(C(C(O1)O)O)O)O)O
  CACTVS 3.370: OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C@@H]1O
  CACTVS 3.370: OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
  OpenEye OEToolkits 1.7.6: C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O)O
  ACDLabs 12.01: OC1C(O)C(OC(O)C1O)CO
• Formula: C6 H12 O6
• Name: beta-D-glucopyranose;
  beta-D-glucose;
  D-glucose;
  glucose
• ChEMBL: CHEMBL1614854
• DrugBank: DB02379
• ZINC: ZINC000003833800
• PDB chain: 3u4a Chain B Residue 776

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3u4a From soil to structure: a novel dimeric family 3-beta--glucosidase isolated from compost using metagenomic analysis
• Resolution: 2.196 Å
• Binding residue (original residue number in PDB): D84 F128 R142 K181 M225 N261 Y262 E488
• Binding residue (residue number reindexed from 1): D83 F127 R141 K180 M224 N260 Y261 E487
• Annotation score: 4

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Feb 21 18:24:29 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>()

   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 = '3u4a', asym_id = 'B', bs = 'BS03', title = 'From soil to structure: a novel dimeric family 3... isolated from compost using metagenomic analysis'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='3u4a', asym_id='B', bs='BS03', title='From soil to structure: a novel dimeric family 3... isolated from compost using metagenomic analysis')

   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 = '0004553,0005975', uniprot = '', pdbid = '3u4a', asym_id = 'B'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0004553,0005975', uniprot='', pdbid='3u4a', asym_id='B')

    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>