Structure of PDB 6nd3 Chain F Binding Site BS01

Receptor Information
>6nd3 Chain F (length=794) Species: 207559 (Oleidesulfovibrio alaskensis G20) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GIPDGPTPRHVKLKENFLKQVPSITVQRAVAITKIAKENPGLPKPLLRAK
TFRYCCETAPLVIQDHELIVGSPNGAPRAGAFSPEVAWRWLQDELDTIGS
RPQDPFYISEEDKKVLREEVFPFWQNKSVDEFCEGQYREADLWEMSGESF
VSDCSYHAVNGGGDSNPGYDVILMKKGMLDIQREAREKLEQLDYANPEDI
DKIYFYKSVIETAEGVMIYARRLSAYAAELAARETDPRRKAELQKISEVN
ARVPAHAPSNFWEAIQAVWTVESLLVVEENQTGMSIGRVDQYMYPFYRAD
IDSGRLTEYEAFDLAGCMLVKMSEMMWITSEGASKFFAGYQPFVNMCVGG
VTREGHDATNDLTYMLMDAVRHVRIYQPTLATRVHNKSPQKYLKKIVDVI
RSGMGFPAVHFDDAHIKMMLAKGVSIEDARDYCLMGCVEPQKSGRLYQWT
STGYTQWPICIELVLNHGVPLWYGKKVTPDMGDLSQYDTYEKFEAAVKEQ
IRWITKNTSVATVISQRAHRELAPKPLMSLMYEGCMESGRDVSAGGAMYN
FGPGVVWSGLATYVDSMAAIKKLVYDDRKYTLAQLNEALKADFAGYDQIL
ADCLAAPKYGNDDDYADMIAADLVHFTETEHRKYKTLYSVLSHGTLSISN
NTPFGQLLGASANGRRAWMPLSDGISPTQGADYKGPTAIIKSVSKMANDN
MNIGMVHNFKLMSGLLDTPEGENGLITLIRTACMLGNGEMQFNYLDNELL
LDAQKHPEKYRDLVVRVAGYSAFFVELCKDVQDEIISRTMLHGF
Ligand information
Ligand IDBTL
InChIInChI=1S/C5H12NO/c1-6(2,3)4-5-7/h5H,4H2,1-3H3/q+1
InChIKeySXKNCCSPZDCRFD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=CC[N+](C)(C)C
CACTVS 3.341
OpenEye OEToolkits 1.5.0		C[N+](C)(C)CC=O
FormulaC5 H12 N O
NameBETAINE ALDEHYDE;
[FORMYLMETHYL]TRIMETHYL-AMMONIUM;
N,N,N-TRIMETHYL AMMONIUM ACETALDEHYDE
ChEMBLCHEMBL1231491
DrugBankDB04401
ZINCZINC000100015771
PDB chain6nd3 Chain F Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6nd3 Structure-Guided Identification of a Small Molecule That Inhibits Anaerobic Choline Metabolism by Human Gut Bacteria.
Resolution2.364 Å
Binding residue
(original residue number in PDB)		Y208 F395 G488 C489 E491 T502 Y506
Binding residue
(residue number reindexed from 1)		Y156 F343 G436 C437 E439 T450 Y454
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) F395 G488 C489 G821
Catalytic site (residue number reindexed from 1) F343 G436 C437 G769
Enzyme Commision number 4.3.99.4: choline trimethylamine-lyase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0016829 lyase activity
GO:0016840 carbon-nitrogen lyase activity
GO:0033265 choline binding
GO:0042803 protein homodimerization activity
Biological Process
GO:0042426 choline catabolic process
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6nd3, PDBe:6nd3, PDBj:6nd3
PDBsum6nd3
PubMed30557011
UniProtQ30W70|CUTC_OLEA2 Choline trimethylamine-lyase (Gene Name=cutC)

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