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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

5QJM

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z328695024

Functional Information from GO Data
ChainGOidnamespacecontents
A0000287molecular_functionmagnesium ion binding
A0003723molecular_functionRNA binding
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005829cellular_componentcytosol
A0006139biological_processnucleobase-containing compound metabolic process
A0006338biological_processchromatin remodeling
A0006753biological_processnucleoside phosphate metabolic process
A0009117biological_processnucleotide metabolic process
A0009191biological_processribonucleoside diphosphate catabolic process
A0016740molecular_functiontransferase activity
A0016779molecular_functionnucleotidyltransferase activity
A0016787molecular_functionhydrolase activity
A0017110molecular_functionnucleoside diphosphate phosphatase activity
A0019144molecular_functionADP-sugar diphosphatase activity
A0019303biological_processD-ribose catabolic process
A0019693biological_processribose phosphate metabolic process
A0030515molecular_functionsnoRNA binding
A0042802molecular_functionidentical protein binding
A0042803molecular_functionprotein homodimerization activity
A0044715molecular_function8-oxo-dGDP phosphatase activity
A0046872molecular_functionmetal ion binding
A0047631molecular_functionADP-ribose diphosphatase activity
A0055086biological_processnucleobase-containing small molecule metabolic process
A0070062cellular_componentextracellular exosome
A0140933molecular_function5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
A1990966biological_processATP generation from poly-ADP-D-ribose
B0000287molecular_functionmagnesium ion binding
B0003723molecular_functionRNA binding
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005829cellular_componentcytosol
B0006139biological_processnucleobase-containing compound metabolic process
B0006338biological_processchromatin remodeling
B0006753biological_processnucleoside phosphate metabolic process
B0009117biological_processnucleotide metabolic process
B0009191biological_processribonucleoside diphosphate catabolic process
B0016740molecular_functiontransferase activity
B0016779molecular_functionnucleotidyltransferase activity
B0016787molecular_functionhydrolase activity
B0017110molecular_functionnucleoside diphosphate phosphatase activity
B0019144molecular_functionADP-sugar diphosphatase activity
B0019303biological_processD-ribose catabolic process
B0019693biological_processribose phosphate metabolic process
B0030515molecular_functionsnoRNA binding
B0042802molecular_functionidentical protein binding
B0042803molecular_functionprotein homodimerization activity
B0044715molecular_function8-oxo-dGDP phosphatase activity
B0046872molecular_functionmetal ion binding
B0047631molecular_functionADP-ribose diphosphatase activity
B0055086biological_processnucleobase-containing small molecule metabolic process
B0070062cellular_componentextracellular exosome
B0140933molecular_function5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
B1990966biological_processATP generation from poly-ADP-D-ribose
C0000287molecular_functionmagnesium ion binding
C0003723molecular_functionRNA binding
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005829cellular_componentcytosol
C0006139biological_processnucleobase-containing compound metabolic process
C0006338biological_processchromatin remodeling
C0006753biological_processnucleoside phosphate metabolic process
C0009117biological_processnucleotide metabolic process
C0009191biological_processribonucleoside diphosphate catabolic process
C0016740molecular_functiontransferase activity
C0016779molecular_functionnucleotidyltransferase activity
C0016787molecular_functionhydrolase activity
C0017110molecular_functionnucleoside diphosphate phosphatase activity
C0019144molecular_functionADP-sugar diphosphatase activity
C0019303biological_processD-ribose catabolic process
C0019693biological_processribose phosphate metabolic process
C0030515molecular_functionsnoRNA binding
C0042802molecular_functionidentical protein binding
C0042803molecular_functionprotein homodimerization activity
C0044715molecular_function8-oxo-dGDP phosphatase activity
C0046872molecular_functionmetal ion binding
C0047631molecular_functionADP-ribose diphosphatase activity
C0055086biological_processnucleobase-containing small molecule metabolic process
C0070062cellular_componentextracellular exosome
C0140933molecular_function5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
C1990966biological_processATP generation from poly-ADP-D-ribose
D0000287molecular_functionmagnesium ion binding
D0003723molecular_functionRNA binding
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0005829cellular_componentcytosol
D0006139biological_processnucleobase-containing compound metabolic process
D0006338biological_processchromatin remodeling
D0006753biological_processnucleoside phosphate metabolic process
D0009117biological_processnucleotide metabolic process
D0009191biological_processribonucleoside diphosphate catabolic process
D0016740molecular_functiontransferase activity
D0016779molecular_functionnucleotidyltransferase activity
D0016787molecular_functionhydrolase activity
D0017110molecular_functionnucleoside diphosphate phosphatase activity
D0019144molecular_functionADP-sugar diphosphatase activity
D0019303biological_processD-ribose catabolic process
D0019693biological_processribose phosphate metabolic process
D0030515molecular_functionsnoRNA binding
D0042802molecular_functionidentical protein binding
D0042803molecular_functionprotein homodimerization activity
D0044715molecular_function8-oxo-dGDP phosphatase activity
D0046872molecular_functionmetal ion binding
D0047631molecular_functionADP-ribose diphosphatase activity
D0055086biological_processnucleobase-containing small molecule metabolic process
D0070062cellular_componentextracellular exosome
D0140933molecular_function5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
D1990966biological_processATP generation from poly-ADP-D-ribose
Functional Information from PDB Data
site_idAC1
Number of Residues8
Detailsbinding site for residue MG A 301
ChainResidue
AALA96
AGLU116
AGLU166
AMG302
AHOH405
AHOH427
AHOH446
AHOH451
site_idAC2
Number of Residues7
Detailsbinding site for residue MG A 302
ChainResidue
AGLU116
AGLU166
AMG301
AHOH403
AHOH446
AHOH448
AGLU112
site_idAC3
Number of Residues6
Detailsbinding site for residue K1G A 303
ChainResidue
ATRP46
AGLU47
AGLY135
BTRP28
BVAL29
BARG51
site_idAC4
Number of Residues5
Detailsbinding site for residue EDO B 302
ChainResidue
BGLN69
BASN149
BASP151
BHOH403
BHOH405
site_idAC5
Number of Residues7
Detailsbinding site for residue MG B 303
ChainResidue
BALA96
BGLU116
BMG304
BHOH412
BHOH415
BHOH432
BHOH448
site_idAC6
Number of Residues8
Detailsbinding site for residue MG B 304
ChainResidue
BGLU112
BGLU115
BGLU116
BGLU166
BMG303
BHOH401
BHOH432
BHOH440
site_idAC7
Number of Residues4
Detailsbinding site for residue K1G B 305
ChainResidue
ATRP28
AARG51
BTRP46
BGLU47
site_idAC8
Number of Residues5
Detailsbinding site for residue EDO B 306
ChainResidue
AARG51
ACYS139
BASP133
BHOH408
BHOH428
site_idAC9
Number of Residues5
Detailsbinding site for residue EDO C 301
ChainResidue
CASP122
CASP152
CGLU154
CASN155
CHOH419
site_idAD1
Number of Residues9
Detailsbinding site for residue MG C 302
ChainResidue
CALA96
CGLU112
CGLU116
CGLU166
CMG303
CHOH415
CHOH417
CHOH426
CHOH447
site_idAD2
Number of Residues8
Detailsbinding site for residue MG C 303
ChainResidue
CALA96
CGLU116
CGLU166
CMG302
CHOH416
CHOH422
CHOH426
CHOH446
site_idAD3
Number of Residues5
Detailsbinding site for residue K1G C 304
ChainResidue
CTRP46
CGLU47
DTRP28
DVAL29
DARG51
site_idAD4
Number of Residues7
Detailsbinding site for residue MG D 301
ChainResidue
DALA96
DGLU116
DGLU166
DMG302
DHOH404
DHOH407
DHOH422
site_idAD5
Number of Residues9
Detailsbinding site for residue MG D 302
ChainResidue
DALA96
DGLY97
DGLU112
DGLU116
DGLU166
DMG301
DHOH404
DHOH417
DHOH422
site_idAD6
Number of Residues5
Detailsbinding site for residue K1G D 303
ChainResidue
CTRP28
CARG51
DTRP46
DGLU47
DGLY135
Functional Information from PROSITE/UniProt
site_idPS00893
Number of Residues22
DetailsNUDIX_BOX Nudix box signature. GliddgEtpeaAAlRELeEEtG
ChainResidueDetails
AGLY97-GLY118
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues420
DetailsDomain: {"description":"Nudix hydrolase","evidences":[{"source":"PROSITE-ProRule","id":"PRU00794","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues84
DetailsMotif: {"description":"Nudix box"}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues8
DetailsBinding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"17052728","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18462755","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21768126","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues24
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"17052728","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18462755","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21768126","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues8
DetailsBinding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"17052728","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues4
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"27257257","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues4
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"15592455","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues8
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

238895

PDB entries from 2025-07-16

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