Structure of PDB 3bm4 Chain B

Receptor sequence
>3bm4B (length=197) Species: 9606 (Homo sapiens) [Search protein sequence]
GKQYIISEELISEGKWVKLEKTTYMDPTGKTRTWESVKRTTRKEQTADGV
AVIPVLQRTLHYECIVLVKQFRPPMGGYCIEFPAGLIDDGETPEAAALRE
LEEETGYKGDIAECSPAVCMDPGLSNCTIHIVTVTINGDDAENARPKPKP
GDGEFVEVISLPKNDLLQRLDALVAEEHLTVDARVYSYALALKHANA
3D structure
PDB3bm4 Molecular Mechanism of ADP-Ribose Hydrolysis By Human NUDT5 From Structural and Kinetic Studies
ChainB
Resolution2.0 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 2.7.7.96: ADP-D-ribose pyrophosphorylase.
3.6.1.13: ADP-ribose diphosphatase.
3.6.1.58: 8-oxo-dGDP phosphatase.
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 A96 E116 A84 E104
BS02 MG B E112 E116 E166 E100 E104 E154
BS03 ADV B W46 E47 D133 G135 W34 E35 D121 G123
BS04 ADV B W28 R51 R84 A96 G97 L98 W16 R39 R72 A84 G85 L86
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0016462 pyrophosphatase activity
GO:0016740 transferase activity
GO:0016779 nucleotidyltransferase activity
GO:0016787 hydrolase activity
GO:0017110 nucleoside diphosphate phosphatase activity
GO:0019144 ADP-sugar diphosphatase activity
GO:0030515 snoRNA binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0044715 8-oxo-dGDP phosphatase activity
GO:0044716 8-oxo-GDP phosphatase activity
GO:0046872 metal ion binding
GO:0047631 ADP-ribose diphosphatase activity
GO:0140933 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006338 chromatin remodeling
GO:0006753 nucleoside phosphate metabolic process
GO:0009117 nucleotide metabolic process
GO:0009191 ribonucleoside diphosphate catabolic process
GO:0019303 D-ribose catabolic process
GO:0019693 ribose phosphate metabolic process
GO:0055086 nucleobase-containing small molecule metabolic process
GO:1990966 ATP generation from poly-ADP-D-ribose
Cellular Component
GO:0005634 nucleus
GO:0005829 cytosol
GO:0070062 extracellular exosome

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Cellular Component
External links
PDB RCSB:3bm4, PDBe:3bm4, PDBj:3bm4
PDBsum3bm4
PubMed18462755
UniProtQ9UKK9|NUDT5_HUMAN ADP-sugar pyrophosphatase (Gene Name=NUDT5)

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