Structure of PDB 5mi6 Chain A Binding Site BS01

Receptor Information
>5mi6 Chain A (length=688) Species: 226186 (Bacteroides thetaiotaomicron VPI-5482) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKK
GMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYA
LQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFY
GKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFV
WAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQK
QAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNP
SIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLG
PVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTW
KDAIRTILPSAAEELESFAMHNSDLGPNGHGYRREESMDIQPAAERFLKA
FKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFK
LTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPCQPG
VKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMISNVKNLP
LQVKANRVLISPANEVVKWAAGNSVEIELDAIYPGENIQINFEISTDGKE
WKTVDLKQKERLSAGLQKAPVKFVRFTNVSQFVLTIEK
Ligand information
Ligand IDNHT
InChIInChI=1S/C9H16N2O4S/c1-2-10-9-11-5-7(14)6(13)4(3-12)15-8(5)16-9/h4-8,12-14H,2-3H2,1H3,(H,10,11)/t4-,5-,6-,7-,8-/m1/s1
InChIKeyPPAIMZHKIXDJRN-FMDGEEDCSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCNC1=N[CH]2[CH](O)[CH](O)[CH](CO)O[CH]2S1
OpenEye OEToolkits 1.5.0CCNC1=N[C@@H]2[C@H]([C@@H]([C@H](O[C@@H]2S1)CO)O)O
ACDLabs 10.04N1=C(SC2OC(C(O)C(O)C12)CO)NCC
CACTVS 3.341CCNC1=N[C@@H]2[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]2S1
OpenEye OEToolkits 1.5.0CCNC1=NC2C(C(C(OC2S1)CO)O)O
FormulaC9 H16 N2 O4 S
Name(3AR,5R,6S,7R,7AR)-2-(ETHYLAMINO)-5-(HYDROXYMETHYL)-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL
ChEMBLCHEMBL1213603
DrugBank
ZINCZINC000016052637
PDB chain5mi6 Chain A Residue 801 [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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PDB5mi6 Increase of enzyme activity through specific covalent modification with fragments.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		G135 K166 D242 C278 Y282 W337 D344
Binding residue
(residue number reindexed from 1)		G132 K163 D239 C275 Y279 W334 D341
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.30,Kd=50nM
Enzymatic activity
Enzyme Commision number 3.2.1.169: protein O-GlcNAcase.
Gene Ontology
Molecular Function
GO:0015929 hexosaminidase activity
GO:0016231 beta-N-acetylglucosaminidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0042802 identical protein binding
GO:0102571 [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006517 protein deglycosylation
GO:1901135 carbohydrate derivative metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5mi6, PDBe:5mi6, PDBj:5mi6
PDBsum5mi6
PubMed29163914
UniProtQ89ZI2|OGA_BACTN O-GlcNAcase BT_4395 (Gene Name=BT_4395)

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