Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2DSB

Crystal structure of human ADP-ribose pyrophosphatase NUDT5

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0003723	molecular_function	RNA binding
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005829	cellular_component	cytosol
A	0006139	biological_process	nucleobase-containing compound metabolic process
A	0006338	biological_process	chromatin remodeling
A	0006753	biological_process	nucleoside phosphate metabolic process
A	0009117	biological_process	nucleotide metabolic process
A	0009191	biological_process	ribonucleoside diphosphate catabolic process
A	0016462	molecular_function	pyrophosphatase activity
A	0016740	molecular_function	transferase activity
A	0016779	molecular_function	nucleotidyltransferase activity
A	0016787	molecular_function	hydrolase activity
A	0017110	molecular_function	nucleoside diphosphate phosphatase activity
A	0019144	molecular_function	ADP-sugar diphosphatase activity
A	0019303	biological_process	D-ribose catabolic process
A	0019693	biological_process	ribose phosphate metabolic process
A	0030515	molecular_function	snoRNA binding
A	0042802	molecular_function	identical protein binding
A	0042803	molecular_function	protein homodimerization activity
A	0044715	molecular_function	8-oxo-dGDP phosphatase activity
A	0044716	molecular_function	8-oxo-GDP phosphatase activity
A	0046872	molecular_function	metal ion binding
A	0047631	molecular_function	ADP-ribose diphosphatase activity
A	0055086	biological_process	nucleobase-containing small molecule metabolic process
A	0070062	cellular_component	extracellular exosome
A	0140933	molecular_function	5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
A	1990966	biological_process	ATP generation from poly-ADP-D-ribose
B	0000287	molecular_function	magnesium ion binding
B	0003723	molecular_function	RNA binding
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005829	cellular_component	cytosol
B	0006139	biological_process	nucleobase-containing compound metabolic process
B	0006338	biological_process	chromatin remodeling
B	0006753	biological_process	nucleoside phosphate metabolic process
B	0009117	biological_process	nucleotide metabolic process
B	0009191	biological_process	ribonucleoside diphosphate catabolic process
B	0016462	molecular_function	pyrophosphatase activity
B	0016740	molecular_function	transferase activity
B	0016779	molecular_function	nucleotidyltransferase activity
B	0016787	molecular_function	hydrolase activity
B	0017110	molecular_function	nucleoside diphosphate phosphatase activity
B	0019144	molecular_function	ADP-sugar diphosphatase activity
B	0019303	biological_process	D-ribose catabolic process
B	0019693	biological_process	ribose phosphate metabolic process
B	0030515	molecular_function	snoRNA binding
B	0042802	molecular_function	identical protein binding
B	0042803	molecular_function	protein homodimerization activity
B	0044715	molecular_function	8-oxo-dGDP phosphatase activity
B	0044716	molecular_function	8-oxo-GDP phosphatase activity
B	0046872	molecular_function	metal ion binding
B	0047631	molecular_function	ADP-ribose diphosphatase activity
B	0055086	biological_process	nucleobase-containing small molecule metabolic process
B	0070062	cellular_component	extracellular exosome
B	0140933	molecular_function	5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
B	1990966	biological_process	ATP generation from poly-ADP-D-ribose
C	0000287	molecular_function	magnesium ion binding
C	0003723	molecular_function	RNA binding
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005829	cellular_component	cytosol
C	0006139	biological_process	nucleobase-containing compound metabolic process
C	0006338	biological_process	chromatin remodeling
C	0006753	biological_process	nucleoside phosphate metabolic process
C	0009117	biological_process	nucleotide metabolic process
C	0009191	biological_process	ribonucleoside diphosphate catabolic process
C	0016462	molecular_function	pyrophosphatase activity
C	0016740	molecular_function	transferase activity
C	0016779	molecular_function	nucleotidyltransferase activity
C	0016787	molecular_function	hydrolase activity
C	0017110	molecular_function	nucleoside diphosphate phosphatase activity
C	0019144	molecular_function	ADP-sugar diphosphatase activity
C	0019303	biological_process	D-ribose catabolic process
C	0019693	biological_process	ribose phosphate metabolic process
C	0030515	molecular_function	snoRNA binding
C	0042802	molecular_function	identical protein binding
C	0042803	molecular_function	protein homodimerization activity
C	0044715	molecular_function	8-oxo-dGDP phosphatase activity
C	0044716	molecular_function	8-oxo-GDP phosphatase activity
C	0046872	molecular_function	metal ion binding
C	0047631	molecular_function	ADP-ribose diphosphatase activity
C	0055086	biological_process	nucleobase-containing small molecule metabolic process
C	0070062	cellular_component	extracellular exosome
C	0140933	molecular_function	5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
C	1990966	biological_process	ATP generation from poly-ADP-D-ribose
D	0000287	molecular_function	magnesium ion binding
D	0003723	molecular_function	RNA binding
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005829	cellular_component	cytosol
D	0006139	biological_process	nucleobase-containing compound metabolic process
D	0006338	biological_process	chromatin remodeling
D	0006753	biological_process	nucleoside phosphate metabolic process
D	0009117	biological_process	nucleotide metabolic process
D	0009191	biological_process	ribonucleoside diphosphate catabolic process
D	0016462	molecular_function	pyrophosphatase activity
D	0016740	molecular_function	transferase activity
D	0016779	molecular_function	nucleotidyltransferase activity
D	0016787	molecular_function	hydrolase activity
D	0017110	molecular_function	nucleoside diphosphate phosphatase activity
D	0019144	molecular_function	ADP-sugar diphosphatase activity
D	0019303	biological_process	D-ribose catabolic process
D	0019693	biological_process	ribose phosphate metabolic process
D	0030515	molecular_function	snoRNA binding
D	0042802	molecular_function	identical protein binding
D	0042803	molecular_function	protein homodimerization activity
D	0044715	molecular_function	8-oxo-dGDP phosphatase activity
D	0044716	molecular_function	8-oxo-GDP phosphatase activity
D	0046872	molecular_function	metal ion binding
D	0047631	molecular_function	ADP-ribose diphosphatase activity
D	0055086	biological_process	nucleobase-containing small molecule metabolic process
D	0070062	cellular_component	extracellular exosome
D	0140933	molecular_function	5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
D	1990966	biological_process	ATP generation from poly-ADP-D-ribose

Functional Information from PROSITE/UniProt

site_id	PS00893
Number of Residues	22
Details	NUDIX_BOX Nudix box signature. GliddgEtpeaAAlRELeEEtG

Chain	Residue	Details
A	GLY97-GLY118

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	BINDING: in other chain => ECO:0000269\|PubMed:17052728, ECO:0000269\|PubMed:18462755, ECO:0000269\|PubMed:21768126

Chain	Residue	Details
A	TRP28
A	ARG84
B	TRP28
B	ARG84
C	TRP28
C	ARG84
D	TRP28
D	ARG84

site_id	SWS_FT_FI2
Number of Residues	24
Details	BINDING: BINDING => ECO:0000269\|PubMed:17052728, ECO:0000269\|PubMed:18462755, ECO:0000269\|PubMed:21768126

Chain	Residue	Details
A	TRP46
B	GLU112
B	GLU116
B	GLU166
C	TRP46
C	ARG51
C	ALA96
C	GLU112
C	GLU116
C	GLU166
D	TRP46
A	ARG51
D	ARG51
D	ALA96
D	GLU112
D	GLU116
D	GLU166
A	ALA96
A	GLU112
A	GLU116
A	GLU166
B	TRP46
B	ARG51
B	ALA96

site_id	SWS_FT_FI3
Number of Residues	8
Details	BINDING: in other chain => ECO:0000269\|PubMed:17052728

Chain	Residue	Details
A	LEU98
A	ASP133
B	LEU98
B	ASP133
C	LEU98
C	ASP133
D	LEU98
D	ASP133

site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: N-acetylmethionine => ECO:0007744\|PubMed:19413330, ECO:0007744\|PubMed:20068231, ECO:0007744\|PubMed:21406692, ECO:0007744\|PubMed:22223895

Chain	Residue	Details
A	MET1
B	MET1
C	MET1
D	MET1

site_id	SWS_FT_FI5
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:21406692, ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	SER3
B	SER3
C	SER3
D	SER3

site_id	SWS_FT_FI6
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:20068231

Chain	Residue	Details
A	SER10
B	SER10
C	SER10
D	SER10

site_id	SWS_FT_FI7
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0000269\|PubMed:27257257

Chain	Residue	Details
A	THR45
B	THR45
C	THR45
D	THR45

site_id	SWS_FT_FI8
Number of Residues	4
Details	MOD_RES: Phosphotyrosine => ECO:0007744\|PubMed:15592455

Chain	Residue	Details
A	TYR74
B	TYR74
C	TYR74
D	TYR74

site_id	SWS_FT_FI9
Number of Residues	8
Details	MOD_RES: N6-acetyllysine => ECO:0007744\|PubMed:19608861

Chain	Residue	Details
A	LYS210
A	LYS218
B	LYS210
B	LYS218
C	LYS210
C	LYS218
D	LYS210
D	LYS218

site_id	SWS_FT_FI10
Number of Residues	8
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744\|PubMed:28112733

Chain	Residue	Details
A	LYS42
B	LYS42
C	LYS42
D	LYS42

Catalytic Information from CSA

site_id	CSA1
Number of Residues	2
Details	Annotated By Reference To The Literature 1mqw

Chain	Residue	Details
A	ASP164
A	ARG84

site_id	CSA2
Number of Residues	2
Details	Annotated By Reference To The Literature 1mqw

Chain	Residue	Details
B	ASP164
B	ARG84

site_id	CSA3
Number of Residues	2
Details	Annotated By Reference To The Literature 1mqw

Chain	Residue	Details
C	ASP164
C	ARG84

site_id	CSA4
Number of Residues	2
Details	Annotated By Reference To The Literature 1mqw

Chain	Residue	Details
D	ASP164
D	ARG84

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)