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5QJI

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z1899842917

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
A0016462molecular_functionpyrophosphatase activity
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
A0044716molecular_function8-oxo-GDP 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
B0016462molecular_functionpyrophosphatase activity
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
B0044716molecular_function8-oxo-GDP 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
C0016462molecular_functionpyrophosphatase activity
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
C0044716molecular_function8-oxo-GDP 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
D0016462molecular_functionpyrophosphatase activity
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
D0044716molecular_function8-oxo-GDP 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 Residues7
Detailsbinding site for residue MG A 301
ChainResidue
AALA96
AGLU116
AMG302
AHOH424
AHOH425
AHOH441
AHOH448

site_idAC2
Number of Residues7
Detailsbinding site for residue MG A 302
ChainResidue
AGLU166
AMG301
AHOH411
AHOH413
AHOH441
AGLU112
AGLU116

site_idAC3
Number of Residues5
Detailsbinding site for residue EDO B 301
ChainResidue
BGLN69
BASN149
BASP151
BHOH414
BHOH425

site_idAC4
Number of Residues6
Detailsbinding site for residue MG B 302
ChainResidue
BALA96
BGLU116
BHOH402
BHOH433
BHOH440
BHOH443

site_idAC5
Number of Residues7
Detailsbinding site for residue MG B 303
ChainResidue
BGLU112
BGLU115
BGLU116
BGLU166
BHOH412
BHOH427
BHOH443

site_idAC6
Number of Residues5
Detailsbinding site for residue K1A B 304
ChainResidue
ATRP28
AARG51
ALEU98
BTRP46
BGLU47

site_idAC7
Number of Residues4
Detailsbinding site for residue EDO B 305
ChainResidue
AARG51
ACYS139
BASP133
BHOH413

site_idAC8
Number of Residues5
Detailsbinding site for residue EDO C 301
ChainResidue
CASP122
CASP152
CGLU154
CASN155
CHOH428

site_idAC9
Number of Residues8
Detailsbinding site for residue MG C 302
ChainResidue
CALA96
CGLU112
CGLU116
CGLU166
CMG303
CHOH404
CHOH408
CHOH461

site_idAD1
Number of Residues7
Detailsbinding site for residue MG C 303
ChainResidue
CALA96
CGLU116
CMG302
CHOH408
CHOH422
CHOH424
CHOH432

site_idAD2
Number of Residues8
Detailsbinding site for residue MG D 301
ChainResidue
DGLN82
DARG84
DALA96
DGLU116
DGLU166
DMG302
DHOH409
DHOH412

site_idAD3
Number of Residues7
Detailsbinding site for residue MG D 302
ChainResidue
DALA96
DGLU112
DGLU116
DGLU166
DMG301
DHOH412
DHOH414

site_idAD4
Number of Residues5
Detailsbinding site for residue K1A 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 Residues8
DetailsBINDING: in other chain => ECO:0000269|PubMed:17052728, ECO:0000269|PubMed:18462755, ECO:0000269|PubMed:21768126
ChainResidueDetails
ATRP28
AARG84
BTRP28
BARG84
CTRP28
CARG84
DTRP28
DARG84

site_idSWS_FT_FI2
Number of Residues24
DetailsBINDING: BINDING => ECO:0000269|PubMed:17052728, ECO:0000269|PubMed:18462755, ECO:0000269|PubMed:21768126
ChainResidueDetails
ATRP46
BGLU112
BGLU116
BGLU166
CTRP46
CARG51
CALA96
CGLU112
CGLU116
CGLU166
DTRP46
AARG51
DARG51
DALA96
DGLU112
DGLU116
DGLU166
AALA96
AGLU112
AGLU116
AGLU166
BTRP46
BARG51
BALA96

site_idSWS_FT_FI3
Number of Residues8
DetailsBINDING: in other chain => ECO:0000269|PubMed:17052728
ChainResidueDetails
ALEU98
AASP133
BLEU98
BASP133
CLEU98
CASP133
DLEU98
DASP133

site_idSWS_FT_FI4
Number of Residues4
DetailsMOD_RES: N-acetylmethionine => ECO:0007744|PubMed:19413330, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:22223895
ChainResidueDetails
AMET1
BMET1
CMET1
DMET1

site_idSWS_FT_FI5
Number of Residues4
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163
ChainResidueDetails
ASER3
BSER3
CSER3
DSER3

site_idSWS_FT_FI6
Number of Residues4
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:20068231
ChainResidueDetails
ASER10
BSER10
CSER10
DSER10

site_idSWS_FT_FI7
Number of Residues4
DetailsMOD_RES: Phosphothreonine => ECO:0000269|PubMed:27257257
ChainResidueDetails
ATHR45
BTHR45
CTHR45
DTHR45

site_idSWS_FT_FI8
Number of Residues4
DetailsMOD_RES: Phosphotyrosine => ECO:0007744|PubMed:15592455
ChainResidueDetails
ATYR74
BTYR74
CTYR74
DTYR74

site_idSWS_FT_FI9
Number of Residues8
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733
ChainResidueDetails
ALYS42
BLYS42
CLYS42
DLYS42

217705

数据于2024-03-27公开中

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