Structure of PDB 3o0f Chain A Binding Site BS01

Receptor Information
>3o0f Chain A (length=287) Species: 367928 (Bifidobacterium adolescentis ATCC 15703) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AEPPAQGWDIHCHTVFSDGTETPRTLVEQARKLGLHGVAIADHDTTAGWD
EATEASEEIGLPLLLGTEITAVDEDVSVHMLAFQYDPSNEHISSMFANTR
AARLRRTKRMVERLSQDFPITWDDVLAQVKEGERTTIGRPHIADALVAAG
VYETRSDAFADAVSAKSKYYIPTPSPSTHEVIAAVKGAGGVVVAAHAGDP
QRNRRLLSDEQLDAMIADGLDGLEVWHRGNPPEQRERLLTIAARHDLLVT
GGSDWHGKGKPNGLGENLTDDDTVREILCRGVDLIGR
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain3o0f Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3o0f Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity.
Resolution1.94 Å
Binding residue
(original residue number in PDB)		D24 R109 R112 G144 R145 P146 R161 S162 F165 K266
Binding residue
(residue number reindexed from 1)		D18 R103 R106 G138 R139 P140 R155 S156 F159 K260
Annotation score4
Enzymatic activity
Enzyme Commision number ?
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

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Molecular Function
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Biological Process
External links
PDB RCSB:3o0f, PDBe:3o0f, PDBj:3o0f
PDBsum3o0f
PubMed21538547
UniProtA1A2L3

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