Structure of PDB 1g1a Chain B Binding Site BS01

Receptor Information

>1g1a Chain B (length=352) Species: 90371 (Salmonella enterica subsp. enterica serovar Typhimurium)

MKILITGGAGFIGSAVVRHIIKNTQDTVVNIDKLTYAGNLESLSDISESN
RYNFEHADICDSAEITRIFEQYQPDAVMHLAAESHVDRSITGPAAFIETN
IVGTYALLEVARKYWSALGEDKKNNFRFHHISTDEVYGDLPHPDEVENSV
TLPLFTETTAYAPSSPYSASKASSDHLVRAWRRTYGLPTIVTNCSNNYGP
YHFPEKLIPLVILNALEGKPLPIYGKGDQIRDWLYVEDHARALHMVVTEG
KAGETYNIGGHNEKKNLDVVFTICDLLDEIVPKATSYREQITYVADRPGH
DRRYAIDAGKISRELGWKPLETFESGIRKTVEWYLANTQWVNNVKSGAYQ
SW

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: 1g1a Chain B Residue 500

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1g1a The crystal structure of dTDP-D-Glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar Typhimurium, the second enzyme in the dTDP-l-rhamnose pathway.
• Resolution: 2.47 Å
• Binding residue (original residue number in PDB): G7 G10 F11 I12 D32 K33 L34 T35 D58 I59 L80 A81 A82 T99 I131 S132 T133 Y167 K171 C194
• Binding residue (residue number reindexed from 1): G7 G10 F11 I12 D32 K33 L34 T35 D58 I59 L80 A81 A82 T99 I131 S132 T133 Y167 K171 C194
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): T133 D134 E135 L152 L154 F155 T158 Y167 K171
• Catalytic site (residue number reindexed from 1): T133 D134 E135 L152 L154 F155 T158 Y167 K171
• 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:1g1a, PDBe:1g1a, PDBj:1g1a
• PDBsum: 1g1a
• PubMed: 11243820
• UniProt: Q9EU31