Structure of PDB 2yb1 Chain A Binding Site BS05

Receptor Information

>2yb1 Chain A (length=284) Species: 536 (Chromobacterium violaceum)

ANIDLHFHSRTSDGALTPTEVIDRAAARAPALLALTDHDCTGGLAEAAAA
AARRGIPFLNGVEVSVSWGRHTVHIVGLGIDPAEPALAAGLKSIREGRLE
RARQMGASLEAAGIAGCFDGAMRWCDNPEMISRTHFARHLVDSGAVKDMR
TVFRKYLTPGKPGYVSHQWASLEDAVGWIVGAGGMAVIAHPGRYDMGRTL
IERLILDFQAAGGQGIEVASGSHSLDDMHKFALHADRHGLYASSGSDFHA
PGEDVGHTEDLPPICRPIWRELEARILRPADAEN

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: 2yb1 Chain A Residue 1293

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2yb1 Prospecting for Unannotated Enzymes: Discovery of a 3',5'-Nucleotide Bisphosphate Phosphatase within the Amidohydrolase Superfamily.
• Resolution: 1.898 Å
• Binding residue (original residue number in PDB): H7 H9 H39 E64 H75 H191 R194 D248 H250
• Binding residue (residue number reindexed from 1): H6 H8 H38 E63 H74 H190 R193 D247 H249
• Annotation score: 1

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

External links

• PDB: RCSB:2yb1, PDBe:2yb1, PDBj:2yb1
• PDBsum: 2yb1
• PubMed: 24401123
• UniProt: Q7NXD4|35NBP_CHRVO 3',5'-nucleoside bisphosphate phosphatase (Gene Name=CV_1693)