Structure of PDB 1ker Chain B Binding Site BS02

Receptor Information

>1ker Chain B (length=347) Species: 1307 (Streptococcus suis)

SQFKNIIVTGGAGFIGSNFVHYVYNNHPDVHVTVLDKLTYAGNKANLEAI
LGDRVELVVGDIADAELVDKLAAKADAIVHYAAESHNDNSLNDPSPFIHT
NFIGTYTLLEAARKYDIRFHHVSTDEVYGDLPLREDLPGHGEGPGEKFTA
ETNYNPSSPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKF
IPRQITNILAGIKPKLYGEGKNVRDWIHTNDHSTGVWAILTKGRMGETYL
IGADGEKNNKEVLELILEKMGQPKDAYDHVTDRAGHDLRYAIDASKLRDE
LGWTPQFTDFSEGLEETIQWYTDNQDWWKAEKEAVEANYAKTQEVIK

Ligand information

• Ligand ID: NAD
• InChI: InChI=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
• InChIKey: BAWFJGJZGIEFAR-NNYOXOHSSA-N
• SMILES:
  CACTVS 3.341: NC(=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 1.5.0: c1cc(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 3.341: NC(=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 1.5.0: c1cc(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
• Formula: C21 H27 N7 O14 P2
• Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
• ChEMBL: CHEMBL1234613
• DrugBank: DB14128
• PDB chain: 1ker Chain B Residue 1500

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1ker Toward a structural understanding of the dehydratase mechanism.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): G14 F15 I16 D37 K38 L39 T40 G43 D62 I63 Y82 A83 A84 S86 T101 S124 T125 Y161 K165 C188 N191
• Binding residue (residue number reindexed from 1): G13 F14 I15 D36 K37 L38 T39 G42 D61 I62 Y81 A82 A83 S85 T100 S123 T124 Y160 K164 C187 N190
• Annotation score: 1

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:0000166 nucleotide binding
• GO:0008460 dTDP-glucose 4,6-dehydratase activity
• GO:0016829 lyase activity

Biological Process

• GO:0009225 nucleotide-sugar metabolic process

External links

• PDB: RCSB:1ker, PDBe:1ker, PDBj:1ker
• PDBsum: 1ker
• PubMed: 11796113
• UniProt: Q8GIP9