Structure of PDB 2yb1 Chain A Binding Site BS04

Receptor Information
>2yb1 Chain A (length=284) Species: 536 (Chromobacterium violaceum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ANIDLHFHSRTSDGALTPTEVIDRAAARAPALLALTDHDCTGGLAEAAAA
AARRGIPFLNGVEVSVSWGRHTVHIVGLGIDPAEPALAAGLKSIREGRLE
RARQMGASLEAAGIAGCFDGAMRWCDNPEMISRTHFARHLVDSGAVKDMR
TVFRKYLTPGKPGYVSHQWASLEDAVGWIVGAGGMAVIAHPGRYDMGRTL
IERLILDFQAAGGQGIEVASGSHSLDDMHKFALHADRHGLYASSGSDFHA
PGEDVGHTEDLPPICRPIWRELEARILRPADAEN
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 chain2yb1 Chain A Residue 1292 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2yb1 Prospecting for Unannotated Enzymes: Discovery of a 3',5'-Nucleotide Bisphosphate Phosphatase within the Amidohydrolase Superfamily.
Resolution1.898 Å
Binding residue
(original residue number in PDB)		H39 R99 R102 S133 R134 T135 F154
Binding residue
(residue number reindexed from 1)		H38 R98 R101 S132 R133 T134 F153
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.3.97: 3',5'-nucleoside bisphosphate phosphatase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003824 catalytic activity
GO:0004534 5'-3' RNA exonuclease activity
GO:0016787 hydrolase activity
GO:0030145 manganese ion binding
GO:0035312 5'-3' DNA exonuclease activity
GO:0046872 metal ion binding
GO:0097657 3',5'-nucleotide bisphosphate phosphatase activity
Biological Process
GO:0006259 DNA metabolic process
GO:0016311 dephosphorylation

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Molecular Function
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Biological Process
External links
PDB RCSB:2yb1, PDBe:2yb1, PDBj:2yb1
PDBsum2yb1
PubMed24401123
UniProtQ7NXD4|35NBP_CHRVO 3',5'-nucleoside bisphosphate phosphatase (Gene Name=CV_1693)

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