Structure of PDB 1l4m Chain A Binding Site BS02

Receptor Information

>1l4m Chain A (length=346) Species: 28901 (Salmonella enterica)

LHALLRDIPAPDAEAMARTQQHIDGLLKPPGSLGRLETLAVQLAGMPGLN
GTPQVGEKAVLVMCADHGVWDEGVAVSPKIVTAIQAANMTRGTTGVCVLA
AQAGAKVHVIDVGIDAEPIPGVVNMRVARGCGNIAVGPAMSRLQAEALLL
EVSRYTCDLAQRGVTLFGVGELGMANTTPAAAMVSVFTGSDAKEVVGIGA
NLPPSRIDNKVDVVRRAIAINQPNPRDGIDVLSKVGGFDLVGMTGVMLGA
ARCGLPVLLDGFLSYSAALAACQIAPAVRPYLIPSHFSAEKGARIALAHL
SMEPYLHMAMRLGEGSGAALAMPIVEAACAMFHNMGELAASNIVLP

Ligand information

• Ligand ID: NCN
• InChI: InChI=1S/C11H14NO9P/c13-8-7(5-20-22(17,18)19)21-10(9(8)14)12-3-1-2-6(4-12)11(15)16/h1-4,7-10,13-14H,5H2,(H2-,15,16,17,18,19)/t7-,8-,9-,10-/m1/s1
• InChIKey: JOUIQRNQJGXQDC-ZYUZMQFOSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)(O)[O-])O)O)C(=O)O
  ACDLabs 10.04: [O-]P(=O)(O)OCC2OC([n+]1cc(ccc1)C(=O)O)C(O)C2O
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)[O-])O)O)C(=O)O
  CACTVS 3.341: O[CH]1[CH](O)[CH](O[CH]1CO[P](O)([O-])=O)[n+]2cccc(c2)C(O)=O
  CACTVS 3.341: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)([O-])=O)[n+]2cccc(c2)C(O)=O
• Formula: C11 H14 N O9 P
• Name: NICOTINATE MONONUCLEOTIDE;
  NAMN
• DrugBank: DB02382
• PDB chain: 1l4m Chain A Residue 991

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1l4m Capture of a labile substrate by expulsion of water molecules from the active site of nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) from Salmonella enterica.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): E174 G176 M177 A178 N179 T180 G202 A203 G264 F265 L266 S291 R314 L315 G316
• Binding residue (residue number reindexed from 1): E171 G173 M174 A175 N176 T177 G199 A200 G261 F262 L263 S288 R311 L312 G313
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): E174 E317
• Catalytic site (residue number reindexed from 1): E171 E314
• Enzyme Commision number: 2.4.2.21: nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0008939 nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity
• GO:0016757 glycosyltransferase activity

Biological Process

• GO:0009236 cobalamin biosynthetic process

External links

• PDB: RCSB:1l4m, PDBe:1l4m, PDBj:1l4m
• PDBsum: 1l4m
• PubMed: 12101181
• UniProt: Q05603|COBT_SALTY Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase (Gene Name=cobT)