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3O4F

Crystal Structure of Spermidine Synthase from E. coli

Replaces:  3ADNReplaces:  3HH9
Functional Information from GO Data
ChainGOidnamespacecontents
A0003824molecular_functioncatalytic activity
A0004766molecular_functionspermidine synthase activity
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0006596biological_processpolyamine biosynthetic process
A0008295biological_processspermidine biosynthetic process
A0010487molecular_functionthermospermine synthase activity
A0016740molecular_functiontransferase activity
A0016768molecular_functionspermine synthase activity
A0042803molecular_functionprotein homodimerization activity
A0043918molecular_functioncadaverine aminopropyltransferase activity
B0003824molecular_functioncatalytic activity
B0004766molecular_functionspermidine synthase activity
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0006596biological_processpolyamine biosynthetic process
B0008295biological_processspermidine biosynthetic process
B0010487molecular_functionthermospermine synthase activity
B0016740molecular_functiontransferase activity
B0016768molecular_functionspermine synthase activity
B0042803molecular_functionprotein homodimerization activity
B0043918molecular_functioncadaverine aminopropyltransferase activity
C0003824molecular_functioncatalytic activity
C0004766molecular_functionspermidine synthase activity
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0006596biological_processpolyamine biosynthetic process
C0008295biological_processspermidine biosynthetic process
C0010487molecular_functionthermospermine synthase activity
C0016740molecular_functiontransferase activity
C0016768molecular_functionspermine synthase activity
C0042803molecular_functionprotein homodimerization activity
C0043918molecular_functioncadaverine aminopropyltransferase activity
D0003824molecular_functioncatalytic activity
D0004766molecular_functionspermidine synthase activity
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0006596biological_processpolyamine biosynthetic process
D0008295biological_processspermidine biosynthetic process
D0010487molecular_functionthermospermine synthase activity
D0016740molecular_functiontransferase activity
D0016768molecular_functionspermine synthase activity
D0042803molecular_functionprotein homodimerization activity
D0043918molecular_functioncadaverine aminopropyltransferase activity
E0003824molecular_functioncatalytic activity
E0004766molecular_functionspermidine synthase activity
E0005737cellular_componentcytoplasm
E0005829cellular_componentcytosol
E0006596biological_processpolyamine biosynthetic process
E0008295biological_processspermidine biosynthetic process
E0010487molecular_functionthermospermine synthase activity
E0016740molecular_functiontransferase activity
E0016768molecular_functionspermine synthase activity
E0042803molecular_functionprotein homodimerization activity
E0043918molecular_functioncadaverine aminopropyltransferase activity
F0003824molecular_functioncatalytic activity
F0004766molecular_functionspermidine synthase activity
F0005737cellular_componentcytoplasm
F0005829cellular_componentcytosol
F0006596biological_processpolyamine biosynthetic process
F0008295biological_processspermidine biosynthetic process
F0010487molecular_functionthermospermine synthase activity
F0016740molecular_functiontransferase activity
F0016768molecular_functionspermine synthase activity
F0042803molecular_functionprotein homodimerization activity
F0043918molecular_functioncadaverine aminopropyltransferase activity
G0003824molecular_functioncatalytic activity
G0004766molecular_functionspermidine synthase activity
G0005737cellular_componentcytoplasm
G0005829cellular_componentcytosol
G0006596biological_processpolyamine biosynthetic process
G0008295biological_processspermidine biosynthetic process
G0010487molecular_functionthermospermine synthase activity
G0016740molecular_functiontransferase activity
G0016768molecular_functionspermine synthase activity
G0042803molecular_functionprotein homodimerization activity
G0043918molecular_functioncadaverine aminopropyltransferase activity
H0003824molecular_functioncatalytic activity
H0004766molecular_functionspermidine synthase activity
H0005737cellular_componentcytoplasm
H0005829cellular_componentcytosol
H0006596biological_processpolyamine biosynthetic process
H0008295biological_processspermidine biosynthetic process
H0010487molecular_functionthermospermine synthase activity
H0016740molecular_functiontransferase activity
H0016768molecular_functionspermine synthase activity
H0042803molecular_functionprotein homodimerization activity
H0043918molecular_functioncadaverine aminopropyltransferase activity
Functional Information from PDB Data
site_idAC1
Number of Residues1
DetailsBINDING SITE FOR RESIDUE SO4 A 289
ChainResidue
AARG243

site_idAC2
Number of Residues2
DetailsBINDING SITE FOR RESIDUE SO4 A 290
ChainResidue
AARG97
AARG262

site_idAC3
Number of Residues3
DetailsBINDING SITE FOR RESIDUE SO4 A 291
ChainResidue
AASN265
APRO266
AALA267

site_idAC4
Number of Residues7
DetailsBINDING SITE FOR RESIDUE SO4 A 292
ChainResidue
ESER168
ELEU169
EPHE170
ETHR171
AHIS12
AASP13
AGLN14

site_idAC5
Number of Residues2
DetailsBINDING SITE FOR RESIDUE SO4 B 289
ChainResidue
BARG97
BARG262

site_idAC6
Number of Residues1
DetailsBINDING SITE FOR RESIDUE SO4 C 289
ChainResidue
CARG243

site_idAC7
Number of Residues1
DetailsBINDING SITE FOR RESIDUE SO4 C 290
ChainResidue
CARG97

site_idAC8
Number of Residues7
DetailsBINDING SITE FOR RESIDUE SO4 C 291
ChainResidue
CSER168
CLEU169
CPHE170
CTHR171
GHIS12
GASP13
GGLN14

site_idAC9
Number of Residues2
DetailsBINDING SITE FOR RESIDUE SO4 C 292
ChainResidue
BTHR171
CLYS135

site_idBC1
Number of Residues2
DetailsBINDING SITE FOR RESIDUE SO4 C 293
ChainResidue
CGLN191
CTYR226

site_idBC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE SO4 C 294
ChainResidue
CHIS12
CASP13
CGLN14
GSER168
GLEU169
GPHE170
GTHR171

site_idBC3
Number of Residues1
DetailsBINDING SITE FOR RESIDUE SO4 D 289
ChainResidue
DARG243

site_idBC4
Number of Residues2
DetailsBINDING SITE FOR RESIDUE SO4 D 290
ChainResidue
DARG97
DARG262

site_idBC5
Number of Residues2
DetailsBINDING SITE FOR RESIDUE SO4 D 291
ChainResidue
DASN23
DVAL24

site_idBC6
Number of Residues1
DetailsBINDING SITE FOR RESIDUE SO4 D 292
ChainResidue
DGLN147

site_idBC7
Number of Residues1
DetailsBINDING SITE FOR RESIDUE SO4 E 289
ChainResidue
EARG243

site_idBC8
Number of Residues7
DetailsBINDING SITE FOR RESIDUE SO4 E 290
ChainResidue
ASER168
ALEU169
APHE170
ATHR171
EHIS12
EASP13
EGLN14

site_idBC9
Number of Residues2
DetailsBINDING SITE FOR RESIDUE SO4 E 291
ChainResidue
EARG97
EARG262

site_idCC1
Number of Residues3
DetailsBINDING SITE FOR RESIDUE SO4 E 292
ChainResidue
EPRO184
EASP238
EASN239

site_idCC2
Number of Residues1
DetailsBINDING SITE FOR RESIDUE SO4 F 289
ChainResidue
FARG243

site_idCC3
Number of Residues1
DetailsBINDING SITE FOR RESIDUE SO4 F 290
ChainResidue
FARG262

site_idCC4
Number of Residues1
DetailsBINDING SITE FOR RESIDUE SO4 F 291
ChainResidue
FARG207

site_idCC5
Number of Residues1
DetailsBINDING SITE FOR RESIDUE SO4 F 292
ChainResidue
FGLN191

site_idCC6
Number of Residues1
DetailsBINDING SITE FOR RESIDUE SO4 G 289
ChainResidue
GARG243

site_idCC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE SO4 G 290
ChainResidue
GLEU11
GGLY193
GVAL194
GSO4291

site_idCC8
Number of Residues3
DetailsBINDING SITE FOR RESIDUE SO4 G 291
ChainResidue
GVAL53
GTYR226
GSO4290

site_idCC9
Number of Residues4
DetailsBINDING SITE FOR RESIDUE SO4 G 292
ChainResidue
GPRO184
GGLY185
GASP238
GASN239

site_idDC1
Number of Residues2
DetailsBINDING SITE FOR RESIDUE SO4 G 293
ChainResidue
GARG97
GARG262

site_idDC2
Number of Residues2
DetailsBINDING SITE FOR RESIDUE SO4 H 289
ChainResidue
HARG97
HARG262

site_idDC3
Number of Residues1
DetailsBINDING SITE FOR RESIDUE SO4 H 290
ChainResidue
HARG243

Functional Information from PROSITE/UniProt
site_idPS01330
Number of Residues14
DetailsPABS_1 Polyamine biosynthesis (PABS) domain signature. VLIIGGGdGamLrE
ChainResidueDetails
AVAL81-GLU94

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues8
DetailsActive site: {"description":"Proton acceptor","evidences":[{"source":"HAMAP-Rule","id":"MF_00198","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"23001854","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues62
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00198","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues458
DetailsDomain: {"description":"PABS","evidences":[{"source":"HAMAP-Rule","id":"MF_00198","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

239803

PDB entries from 2025-08-06

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