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Structure of PDB 1ifx Chain A Binding Site BS01

Receptor Information

>1ifx Chain A (length=245) Species: 1423 (Bacillus subtilis)

SMQEKIMRELHVKPSIDPKQEIEDRVNFLKQYVKKTGAKGFVLGISGGQD
STLAGRLAQLAVESIREEGGDAQFIAVRLPHGDDAQLALKFIKPDKSWKF
DIKSTVSAFSDQYQQETGDQLTDFNKGNVKARTRMIAQYAIGGQEGLLVL
GTDHAAEAVTGFFTKYGDGGADLLPLTGLTKRQGRTLLKELGAPERLYLI
SYDEIDDYLEGKEVSAKVSEALEKRYSMTEHKRQVPASMFDDWWK

Ligand information

• Ligand ID: DND
• InChI: InChI=1S/C21H26N6O15P2/c22-17-12-18(24-7-23-17)27(8-25-12)20-16(31)14(29)11(41-20)6-39-44(36,37)42-43(34,35)38-5-10-13(28)15(30)19(40-10)26-3-1-2-9(4-26)21(32)33/h1-4,7-8,10-11,13-16,19-20,28-31H,5-6H2,(H4-,22,23,24,32,33,34,35,36,37)/p+1/t10-,11-,13-,14-,15-,16-,19-,20-/m1/s1
• InChIKey: SENPVEZBRZQVST-HISDBWNOSA-O
• SMILES:
  CACTVS 3.385: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)[n+]5cccc(c5)C(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.7.6: c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)O
  CACTVS 3.385: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)[n+]5cccc(c5)C(O)=O)[CH](O)[CH]3O
  OpenEye OEToolkits 1.7.6: 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)O
• Formula: C21 H27 N6 O15 P2
• Name: NICOTINIC ACID ADENINE DINUCLEOTIDE;
  DEAMIDO-NAD+
• DrugBank: DB04099
• ZINC: ZINC000008216447
• PDB chain: 1ifx Chain A Residue 8000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1ifx Stabilization of active-site loops in NH3-dependent NAD+ synthetase from Bacillus subtilis.
• Resolution: 2.25 Å
• Binding residue (original residue number in PDB): F129 N133 R137 F167 F168 T169 K170 H257 K258
• Binding residue (residue number reindexed from 1): F124 N128 R132 F162 F163 T164 K165 H231 K232
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): D50 E162
• Catalytic site (residue number reindexed from 1): D50 E157
• Enzyme Commision number: 6.3.1.5: NAD(+) synthase.

Gene Ontology

Molecular Function

• GO:0003952 NAD+ synthase (glutamine-hydrolyzing) activity
• GO:0004359 glutaminase activity
• GO:0005524 ATP binding
• GO:0008795 NAD+ synthase activity
• GO:0016874 ligase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0009435 NAD biosynthetic process
• GO:0030435 sporulation resulting in formation of a cellular spore

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:1ifx, PDBe:1ifx, PDBj:1ifx
• PDBsum: 1ifx
• PubMed: 11375500
• UniProt: P08164|NADE_BACSU NH(3)-dependent NAD(+) synthetase (Gene Name=nadE)

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