Structure of PDB 3o0f Chain A Binding Site BS05

Receptor Information

>3o0f Chain A (length=287) Species: 367928 (Bifidobacterium adolescentis ATCC 15703)

AEPPAQGWDIHCHTVFSDGTETPRTLVEQARKLGLHGVAIADHDTTAGWD
EATEASEEIGLPLLLGTEITAVDEDVSVHMLAFQYDPSNEHISSMFANTR
AARLRRTKRMVERLSQDFPITWDDVLAQVKEGERTTIGRPHIADALVAAG
VYETRSDAFADAVSAKSKYYIPTPSPSTHEVIAAVKGAGGVVVAAHAGDP
QRNRRLLSDEQLDAMIADGLDGLEVWHRGNPPEQRERLLTIAARHDLLVT
GGSDWHGKGKPNGLGENLTDDDTVREILCRGVDLIGR

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: 3o0f Chain A Residue 305

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3o0f Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity.
• Resolution: 1.94 Å
• Binding residue (original residue number in PDB): H19 H49 H85 D260 H262 K266
• Binding residue (residue number reindexed from 1): H13 H43 H79 D254 H256 K260
• Annotation score: 3

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003824 catalytic activity
• GO:0004534 5'-3' RNA exonuclease activity
• GO:0035312 5'-3' DNA exonuclease activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006259 DNA metabolic process

External links

• PDB: RCSB:3o0f, PDBe:3o0f, PDBj:3o0f
• PDBsum: 3o0f
• PubMed: 21538547
• UniProt: A1A2L3