Structure of PDB 6vdj Chain A Binding Site BS01

Receptor Information

>6vdj Chain A (length=308) Species: 2041159 (Apicomplexa sp.)

KRPKISLIGSGMIGGTMAYLCALKELGDVVLFDVVKNMPQGKALDLSHST
SVADTNVKVTGTNSYEDIKGSDVVIITAGLTDDLLPINAKIMKEVGENIK
KYCPNAFVICITNPLDVMVKVLQEASGLPHNKVCGMAGVLDSSRFRYFIA
EKLNVSPRDVQAMVIGAHGDNMVPLPRYVTVNGIPLQEFIKKGWITQEEI
DEIVERTRNAGGEIVNLLGTGSAYFAPAASAIAMAEAYLKDQKRVLPCSC
YLEGQYGVKDLYVGVPVVIGGNGVEKVIELELTPEEKEMFDKSIEEVREL
VKALEALD

Ligand information

• Ligand ID: TXD
• InChI: InChI=1S/C21H31N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-2,7-11,13-16,20-21,29-32H,3-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t9?,10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
• InChIKey: GFDCQHGWOHYWLP-BFAIWXBASA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5CC=CC(C5)C(=O)N)O)O)O)O)N
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5CC=CC(C5)C(=O)N)O)O)O)O)N
  CACTVS 3.341: NC(=O)[CH]1CN(CC=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
  CACTVS 3.341: NC(=O)[C@H]1CN(CC=C1)[C@@H]2O[C@H](CO[P@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
• Formula: C21 H31 N7 O14 P2
• Name: 1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
• PDB chain: 6vdj Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vdj Mechanism of Bifunctionality in an Ancestral Apicomplexan Malate/Lactate Dehydrogenase
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): G17 M18 I19 D39 V40 A84 I109 I129 T130 N131 M154 H186
• Binding residue (residue number reindexed from 1): G11 M12 I13 D33 V34 A78 I91 I111 T112 N113 M136 H168
• Annotation score: 1

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sat Nov 16 10:20:25 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 = '6vdj', asym_id = 'A', bs = 'BS01', title = 'Mechanism of Bifunctionality in an Ancestral Apicomplexan Malate/Lactate Dehydrogenase'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='6vdj', asym_id='A', bs='BS01', title='Mechanism of Bifunctionality in an Ancestral Apicomplexan Malate/Lactate Dehydrogenase')

   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 = '0003824,0016491,0016616,0019752', uniprot = '', pdbid = '6vdj', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003824,0016491,0016616,0019752', uniprot='', pdbid='6vdj', 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>