Structure of PDB 1ket Chain A Binding Site BS01

Receptor Information
>1ket Chain A (length=346) Species: 1307 (Streptococcus suis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QFKNIIVTGGAGFIGSNFVHYVYNNHPDVHVTVLDKLTYAGNKANLEAIL
GDRVELVVGDIADAELVDKLAAKADAIVHYAAESHNDNSLNDPSPFIHTN
FIGTYTLLEAARKYDIRFHHVSTDEVYGDLPLREDLPGHGEGPGEKFTAE
TNYNPSSPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKFI
PRQITNILAGIKPKLYGEGKNVRDWIHTNDHSTGVWAILTKGRMGETYLI
GADGEKNNKEVLELILEKMGQPKDAYDHVTDRAGHDLRYAIDASKLRDEL
GWTPQFTDFSEGLEETIQWYTDNQDWWKAEKEAVEANYAKTQEVIK
Ligand information
Ligand IDTYD
InChIInChI=1S/C10H16N2O11P2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(22-8)4-21-25(19,20)23-24(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyUJLXYODCHAELLY-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)OP(=O)(O)O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)O)O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H16 N2 O11 P2
NameTHYMIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL259724
DrugBankDB03103
ZINCZINC000008215882
PDB chain1ket Chain A Residue 2573 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1ket Toward a structural understanding of the dehydratase mechanism.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		E127 N190 F201 R204 Q205 K216 Y218 R225 N260 R284 H287
Binding residue
(residue number reindexed from 1)		E125 N188 F199 R202 Q203 K214 Y216 R223 N258 R282 H285
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) T125 D126 E127 Y161 K165
Catalytic site (residue number reindexed from 1) T123 D124 E125 Y159 K163
Enzyme Commision number 4.2.1.46: dTDP-glucose 4,6-dehydratase.
Gene Ontology
Molecular Function
GO:0008460 dTDP-glucose 4,6-dehydratase activity
GO:0016829 lyase activity
Biological Process
GO:0009103 lipopolysaccharide biosynthetic process
GO:0009225 nucleotide-sugar metabolic process
GO:0019305 dTDP-rhamnose biosynthetic process
GO:0045226 extracellular polysaccharide biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1ket, PDBe:1ket, PDBj:1ket
PDBsum1ket
PubMed11796113
UniProtP95780|RMLB_STRMU dTDP-glucose 4,6-dehydratase (Gene Name=rmlB)

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