Structure of PDB 1ket Chain B Binding Site BS02

Receptor Information
>1ket Chain B (length=346) Species: 1307 (Streptococcus suis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SQFKNIIVTGGAGFIGSNFVHYVYNNHPDVHVTVLDKLTYAGNKANLEAI
LGDRVELVVGDIADAELVDKLAAKADAIVHYAAESHNDNSLNDPSPFIHT
NFIGTYTLLEAARKYDIRFHHVSTDEVYGDLPLREDLPGHGEGPGEKFTA
ETNYNPSSPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKF
IPRQITNILAGIKPKLYGEGKNVRDWIHTNDHSTGVWAILTKGRMGETYL
IGADGEKNNKEVLELILEKMGQPKDAYDHVTDRAGHDLRYAIDASKLRDE
LGWTPQFTDFSEGLEETIQWYTDNQDWWKAEKEAVEANYAKTQEVI
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/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/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](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
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](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
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain1ket Chain B Residue 1500 [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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PDB1ket Toward a structural understanding of the dehydratase mechanism.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		G14 F15 I16 D37 K38 L39 T40 G43 D62 I63 Y82 A84 S86 T101 S124 T125 Y161 K165
Binding residue
(residue number reindexed from 1)		G13 F14 I15 D36 K37 L38 T39 G42 D61 I62 Y81 A83 S85 T100 S123 T124 Y160 K164
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) T125 D126 E127 Y161 K165
Catalytic site (residue number reindexed from 1) T124 D125 E126 Y160 K164
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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