Structure of PDB 4b2o Chain D Binding Site BS01

Receptor Information

>4b2o Chain D (length=264) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

MRILFIGDVVGSPGRDMVKEYVPKLKTKYKPHFTIINGENAAHGKGLTEK
IYHSLIQSGADAITMGNHTWDKKEIFDFIDDVPNLVRPANFPEGTPGKGI
TYVKANGKELAVINLQGRTFLPPLDDPFLKADELIAEAAKRTPYIFIDFH
AEATSEKLALGWYTDGRASAVVGTHTHVQTADNRILPKGTAYITDVGMTG
PYDGILGMDRETIIKRFKTNLPVRFTVAEGKTTLSGVVIDIDDQTKKAVK
IERILINDDHMFFE

Ligand information

• Ligand ID: PO4
• InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
• InChIKey: NBIIXXVUZAFLBC-UHFFFAOYSA-K
• SMILES:
  CACTVS 3.341: [O-][P]([O-])([O-])=O
  ACDLabs 10.04: [O-]P([O-])([O-])=O
  OpenEye OEToolkits 1.5.0: [O-]P(=O)([O-])[O-]
• Formula: O4 P
• Name: PHOSPHATE ION
• DrugBank: DB14523
• PDB chain: 4b2o Chain D Residue 1265

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4b2o The Ymdb Phosphodiesterase is a Global Regulator of Late Adaptive Responses in Bacillus Subtilis.
• Resolution: 1.64 Å
• Binding residue (original residue number in PDB): E39 N40 N67 H68 H175 H177
• Binding residue (residue number reindexed from 1): E39 N40 N67 H68 H175 H177
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.1.4.16: 2',3'-cyclic-nucleotide 2'-phosphodiesterase.

Gene Ontology

Molecular Function

• GO:0004113 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity
• GO:0008663 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:4b2o, PDBe:4b2o, PDBj:4b2o
• PDBsum: 4b2o
• PubMed: 24163345
• UniProt: O31775|YMDB_BACSU 2',3'-cyclic-nucleotide 2'-phosphodiesterase (Gene Name=ymdB)