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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

5BV3

Yeast Scavenger Decapping Enzyme in complex with m7GDP

Functional Information from GO Data
ChainGOidnamespacecontents
A0000288biological_processnuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
A0000290biological_processdeadenylation-dependent decapping of nuclear-transcribed mRNA
A0000340molecular_functionRNA 7-methylguanosine cap binding
A0000932cellular_componentP-body
A0000956biological_processnuclear-transcribed mRNA catabolic process
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005737cellular_componentcytoplasm
A0005739cellular_componentmitochondrion
A0006970biological_processresponse to osmotic stress
A0006979biological_processresponse to oxidative stress
A0007584biological_processresponse to nutrient
A0009267biological_processcellular response to starvation
A0009408biological_processresponse to heat
A0016787molecular_functionhydrolase activity
A0016818molecular_functionhydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
A0030234molecular_functionenzyme regulator activity
A0031086biological_processnuclear-transcribed mRNA catabolic process, deadenylation-independent decay
A0042802molecular_functionidentical protein binding
A0042803molecular_functionprotein homodimerization activity
A0044692molecular_functionexoribonuclease activator activity
A0046982molecular_functionprotein heterodimerization activity
A0048471cellular_componentperinuclear region of cytoplasm
A0050072molecular_functionobsolete m7G(5')pppN diphosphatase activity
A0090342biological_processobsolete regulation of cell aging
A0106095cellular_componentm7G(5')pppN diphosphatase complex
A0140932molecular_function5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity
B0000288biological_processnuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
B0000290biological_processdeadenylation-dependent decapping of nuclear-transcribed mRNA
B0000340molecular_functionRNA 7-methylguanosine cap binding
B0000932cellular_componentP-body
B0000956biological_processnuclear-transcribed mRNA catabolic process
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0005739cellular_componentmitochondrion
B0006970biological_processresponse to osmotic stress
B0006979biological_processresponse to oxidative stress
B0007584biological_processresponse to nutrient
B0009267biological_processcellular response to starvation
B0009408biological_processresponse to heat
B0016787molecular_functionhydrolase activity
B0016818molecular_functionhydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
B0030234molecular_functionenzyme regulator activity
B0031086biological_processnuclear-transcribed mRNA catabolic process, deadenylation-independent decay
B0042802molecular_functionidentical protein binding
B0042803molecular_functionprotein homodimerization activity
B0044692molecular_functionexoribonuclease activator activity
B0046982molecular_functionprotein heterodimerization activity
B0048471cellular_componentperinuclear region of cytoplasm
B0050072molecular_functionobsolete m7G(5')pppN diphosphatase activity
B0090342biological_processobsolete regulation of cell aging
B0106095cellular_componentm7G(5')pppN diphosphatase complex
B0140932molecular_function5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity
C0000288biological_processnuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
C0000290biological_processdeadenylation-dependent decapping of nuclear-transcribed mRNA
C0000340molecular_functionRNA 7-methylguanosine cap binding
C0000932cellular_componentP-body
C0000956biological_processnuclear-transcribed mRNA catabolic process
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005737cellular_componentcytoplasm
C0005739cellular_componentmitochondrion
C0006970biological_processresponse to osmotic stress
C0006979biological_processresponse to oxidative stress
C0007584biological_processresponse to nutrient
C0009267biological_processcellular response to starvation
C0009408biological_processresponse to heat
C0016787molecular_functionhydrolase activity
C0016818molecular_functionhydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
C0030234molecular_functionenzyme regulator activity
C0031086biological_processnuclear-transcribed mRNA catabolic process, deadenylation-independent decay
C0042802molecular_functionidentical protein binding
C0042803molecular_functionprotein homodimerization activity
C0044692molecular_functionexoribonuclease activator activity
C0046982molecular_functionprotein heterodimerization activity
C0048471cellular_componentperinuclear region of cytoplasm
C0050072molecular_functionobsolete m7G(5')pppN diphosphatase activity
C0090342biological_processobsolete regulation of cell aging
C0106095cellular_componentm7G(5')pppN diphosphatase complex
C0140932molecular_function5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity
D0000288biological_processnuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
D0000290biological_processdeadenylation-dependent decapping of nuclear-transcribed mRNA
D0000340molecular_functionRNA 7-methylguanosine cap binding
D0000932cellular_componentP-body
D0000956biological_processnuclear-transcribed mRNA catabolic process
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0005737cellular_componentcytoplasm
D0005739cellular_componentmitochondrion
D0006970biological_processresponse to osmotic stress
D0006979biological_processresponse to oxidative stress
D0007584biological_processresponse to nutrient
D0009267biological_processcellular response to starvation
D0009408biological_processresponse to heat
D0016787molecular_functionhydrolase activity
D0016818molecular_functionhydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
D0030234molecular_functionenzyme regulator activity
D0031086biological_processnuclear-transcribed mRNA catabolic process, deadenylation-independent decay
D0042802molecular_functionidentical protein binding
D0042803molecular_functionprotein homodimerization activity
D0044692molecular_functionexoribonuclease activator activity
D0046982molecular_functionprotein heterodimerization activity
D0048471cellular_componentperinuclear region of cytoplasm
D0050072molecular_functionobsolete m7G(5')pppN diphosphatase activity
D0090342biological_processobsolete regulation of cell aging
D0106095cellular_componentm7G(5')pppN diphosphatase complex
D0140932molecular_function5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity
Functional Information from PDB Data
site_idAC1
Number of Residues16
Detailsbinding site for residue M7G A 401
ChainResidue
ALYS126
ASER263
ATYR264
AHIS270
AHOH532
BASN91
BTYR94
BTRP96
ATRP161
AGLU171
APRO193
AASP194
AMET195
ALYS196
AHIS259
APRO262
site_idAC2
Number of Residues2
Detailsbinding site for residue SO4 A 402
ChainResidue
AASN281
ASER282
site_idAC3
Number of Residues7
Detailsbinding site for residue SO4 A 403
ChainResidue
AASN24
ATHR27
AGLY280
AHOH512
BGLN26
BHIS276
BPRO277
site_idAC4
Number of Residues4
Detailsbinding site for residue SO4 B 401
ChainResidue
BLEU279
BGLY280
BASN281
BSER282
site_idAC5
Number of Residues6
Detailsbinding site for residue SO4 B 402
ChainResidue
BGLN130
BPHE132
BLYS287
BILE315
BGLY316
BHIS319
site_idAC6
Number of Residues15
Detailsbinding site for residue M7G C 401
ChainResidue
CLYS126
CTRP161
CGLU171
CPRO193
CASP194
CMET195
CLYS196
CHIS259
CPRO262
CSER263
CTYR264
CHIS270
DASN91
DTYR94
DTRP96
site_idAC7
Number of Residues4
Detailsbinding site for residue SO4 C 402
ChainResidue
CGLY280
CASN281
CSER282
CHOH501
site_idAC8
Number of Residues1
Detailsbinding site for residue CL C 403
ChainResidue
CARG336
site_idAC9
Number of Residues3
Detailsbinding site for residue SO4 D 401
ChainResidue
DGLY280
DASN281
DSER282
site_idAD1
Number of Residues6
Detailsbinding site for residue SO4 D 402
ChainResidue
DGLN130
DPHE132
DLYS287
DILE315
DGLY316
DHIS319
site_idAD2
Number of Residues1
Detailsbinding site for residue CL D 403
ChainResidue
DARG336
site_idAD3
Number of Residues2
Detailsbinding site for residue CL D 404
ChainResidue
CASN24
DPRO277
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues16
DetailsMotif: {"description":"Histidine triad motif","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues4
DetailsActive site: {"description":"Nucleophile","evidences":[{"source":"UniProtKB","id":"Q96C86","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues6
DetailsBinding site: {"evidences":[{"source":"UniProtKB","id":"Q96C86","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues44
DetailsBinding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues3
DetailsModified residue: {"description":"Phosphothreonine; by YAK1","evidences":[{"source":"PubMed","id":"15240832","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues4
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues4
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

245663

PDB entries from 2025-12-03

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