Structure of PDB 4yih Chain B

Receptor sequence
>4yihB (length=187) Species: 9606 (Homo sapiens) [Search protein sequence]
SVRVLVDMDGVLADFEAGLLRGFRRRFPEEPHVPLEQRRGFLAREQYRAL
RPDLADKVASVYEAPGFFLDLEPIPGALDAVREMNDLPDTQVFICTSPLL
KYHHCVGEKYRWVEQHLGPQFVERIILTRDKTVVLGDLLIDDKDTVRGQE
ETPSWEHILFTCCHNRHLRRRLLSWSDNWREILDSKR
3D structure
PDB4yih Structure-based design of a bisphosphonate 5'(3')-deoxyribonucleotidase inhibitor
ChainB
Resolution1.82 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) D10 D12 D145
Catalytic site (residue number reindexed from 1) D7 D9 D142
Enzyme Commision number 3.1.3.-
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 MG B D10 D12 D145 D7 D9 D142
BS02 2O2 B D12 F18 F44 L45 A46 R47 Y65 L102 L103 R132 D9 F15 F41 L42 A43 R44 Y62 L99 L100 R129 PDBbind-CN: -logKd/Ki=4.66,Ki=21.7uM
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0008252 nucleotidase activity
GO:0008253 5'-nucleotidase activity
GO:0016787 hydrolase activity
GO:0016791 phosphatase activity
GO:0019103 pyrimidine nucleotide binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0050483 IMP 5'-nucleotidase activity
Biological Process
GO:0000255 allantoin metabolic process
GO:0006204 IMP catabolic process
GO:0006249 dCMP catabolic process
GO:0009117 nucleotide metabolic process
GO:0009223 pyrimidine deoxyribonucleotide catabolic process
GO:0009264 deoxyribonucleotide catabolic process
GO:0016311 dephosphorylation
GO:0043605 amide catabolic process
GO:0046050 UMP catabolic process
GO:0046055 dGMP catabolic process
GO:0046074 dTMP catabolic process
GO:0046079 dUMP catabolic process
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4yih, PDBe:4yih, PDBj:4yih
PDBsum4yih
PubMed
UniProtQ8TCD5|NT5C_HUMAN 5'(3')-deoxyribonucleotidase, cytosolic type (Gene Name=NT5C)

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