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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

9Q0O

Cryo-EM structure of PPAT-NUDT5 complex bound to 6-benzylthioinosine-5'-monophosphate (6-benzylTIMP)

This is a non-PDB format compatible entry.
Functional Information from GO Data
ChainGOidnamespacecontents
A0004044molecular_functionamidophosphoribosyltransferase activity
A0005515molecular_functionprotein binding
A0005829cellular_componentcytosol
A0006164biological_processpurine nucleotide biosynthetic process
A0006189biological_process'de novo' IMP biosynthetic process
B0004044molecular_functionamidophosphoribosyltransferase activity
B0005515molecular_functionprotein binding
B0005829cellular_componentcytosol
B0006164biological_processpurine nucleotide biosynthetic process
B0006189biological_process'de novo' IMP biosynthetic process
C0004044molecular_functionamidophosphoribosyltransferase activity
C0005515molecular_functionprotein binding
C0005829cellular_componentcytosol
C0006164biological_processpurine nucleotide biosynthetic process
C0006189biological_process'de novo' IMP biosynthetic process
D0004044molecular_functionamidophosphoribosyltransferase activity
D0005515molecular_functionprotein binding
D0005829cellular_componentcytosol
D0006164biological_processpurine nucleotide biosynthetic process
D0006189biological_process'de novo' IMP biosynthetic process
E0000287molecular_functionmagnesium ion binding
E0005515molecular_functionprotein binding
E0005634cellular_componentnucleus
E0005829cellular_componentcytosol
E0006338biological_processchromatin remodeling
E0006753biological_processnucleoside phosphate metabolic process
E0009117biological_processnucleotide metabolic process
E0009191biological_processribonucleoside diphosphate catabolic process
E0016779molecular_functionnucleotidyltransferase activity
E0017110molecular_functionnucleoside diphosphate phosphatase activity
E0019144molecular_functionADP-sugar pyrophosphatase activity
E0019303biological_processD-ribose catabolic process
E0019693biological_processribose phosphate metabolic process
E0030515molecular_functionsnoRNA binding
E0042802molecular_functionidentical protein binding
E0042803molecular_functionprotein homodimerization activity
E0044715molecular_function8-oxo-dGDP phosphatase activity
E0047631molecular_functionADP-ribose diphosphatase activity
E0055086biological_processnucleobase-containing small molecule metabolic process
E0070062cellular_componentextracellular exosome
E0140933molecular_function5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
E1990966biological_processATP generation from poly-ADP-D-ribose
F0000287molecular_functionmagnesium ion binding
F0005515molecular_functionprotein binding
F0005634cellular_componentnucleus
F0005829cellular_componentcytosol
F0006338biological_processchromatin remodeling
F0006753biological_processnucleoside phosphate metabolic process
F0009117biological_processnucleotide metabolic process
F0009191biological_processribonucleoside diphosphate catabolic process
F0016779molecular_functionnucleotidyltransferase activity
F0017110molecular_functionnucleoside diphosphate phosphatase activity
F0019144molecular_functionADP-sugar pyrophosphatase activity
F0019303biological_processD-ribose catabolic process
F0019693biological_processribose phosphate metabolic process
F0030515molecular_functionsnoRNA binding
F0042802molecular_functionidentical protein binding
F0042803molecular_functionprotein homodimerization activity
F0044715molecular_function8-oxo-dGDP phosphatase activity
F0047631molecular_functionADP-ribose diphosphatase activity
F0055086biological_processnucleobase-containing small molecule metabolic process
F0070062cellular_componentextracellular exosome
F0140933molecular_function5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
F1990966biological_processATP generation from poly-ADP-D-ribose
G0000287molecular_functionmagnesium ion binding
G0005515molecular_functionprotein binding
G0005634cellular_componentnucleus
G0005829cellular_componentcytosol
G0006338biological_processchromatin remodeling
G0006753biological_processnucleoside phosphate metabolic process
G0009117biological_processnucleotide metabolic process
G0009191biological_processribonucleoside diphosphate catabolic process
G0016779molecular_functionnucleotidyltransferase activity
G0017110molecular_functionnucleoside diphosphate phosphatase activity
G0019144molecular_functionADP-sugar pyrophosphatase activity
G0019303biological_processD-ribose catabolic process
G0019693biological_processribose phosphate metabolic process
G0030515molecular_functionsnoRNA binding
G0042802molecular_functionidentical protein binding
G0042803molecular_functionprotein homodimerization activity
G0044715molecular_function8-oxo-dGDP phosphatase activity
G0047631molecular_functionADP-ribose diphosphatase activity
G0055086biological_processnucleobase-containing small molecule metabolic process
G0070062cellular_componentextracellular exosome
G0140933molecular_function5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
G1990966biological_processATP generation from poly-ADP-D-ribose
H0000287molecular_functionmagnesium ion binding
H0005515molecular_functionprotein binding
H0005634cellular_componentnucleus
H0005829cellular_componentcytosol
H0006338biological_processchromatin remodeling
H0006753biological_processnucleoside phosphate metabolic process
H0009117biological_processnucleotide metabolic process
H0009191biological_processribonucleoside diphosphate catabolic process
H0016779molecular_functionnucleotidyltransferase activity
H0017110molecular_functionnucleoside diphosphate phosphatase activity
H0019144molecular_functionADP-sugar pyrophosphatase activity
H0019303biological_processD-ribose catabolic process
H0019693biological_processribose phosphate metabolic process
H0030515molecular_functionsnoRNA binding
H0042802molecular_functionidentical protein binding
H0042803molecular_functionprotein homodimerization activity
H0044715molecular_function8-oxo-dGDP phosphatase activity
H0047631molecular_functionADP-ribose diphosphatase activity
H0055086biological_processnucleobase-containing small molecule metabolic process
H0070062cellular_componentextracellular exosome
H0140933molecular_function5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
H1990966biological_processATP generation from poly-ADP-D-ribose
Functional Information from PROSITE/UniProt
site_idPS00103
Number of Residues13
DetailsPUR_PYR_PR_TRANSFER Purine/pyrimidine phosphoribosyl transferases signature. IVLVDDSIVRGnT
ChainResidueDetails
AILE385-THR397
site_idPS00893
Number of Residues22
DetailsNUDIX_BOX Nudix box signature. GliddgEtpeaAAlRELeEEtG
ChainResidueDetails
EGLY97-GLY118
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues996
DetailsDomain: {"description":"Glutamine amidotransferase type-2","evidences":[{"source":"PROSITE-ProRule","id":"PRU00609","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues4
DetailsActive site: {"description":"Nucleophile","evidences":[{"source":"PROSITE-ProRule","id":"PRU00609","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues28
DetailsBinding site: {"evidences":[{"source":"UniProtKB","id":"P00497","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues560
DetailsDomain: {"description":"Nudix hydrolase","evidences":[{"source":"PROSITE-ProRule","id":"PRU00794","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues84
DetailsMotif: {"description":"Nudix box"}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"21768126","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3L85","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues4
DetailsBinding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"21768126","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3L85","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues12
DetailsBinding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"17052728","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18462755","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2DSC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3BM4","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"17052728","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18462755","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2DSC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3BM4","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues16
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_FI11
Number of Residues4
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"27257257","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues4
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"15592455","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues8
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI14
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

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PDB entries from 2026-07-22

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