Loading
PDBj
MenuPDBj@FacebookPDBj@X(formerly Twitter)PDBj@BlueSkyPDBj@YouTubewwPDB FoundationwwPDBDonate
RCSB PDBPDBeBMRBAdv. SearchSearch help

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
DetailsACT_SITE: Proton acceptor => ECO:0000255|HAMAP-Rule:MF_00198, ECO:0000305|PubMed:23001854
ChainResidueDetails
AASP158
BASP158
CASP158
DASP158
EASP158
FASP158
GASP158
HASP158

site_idSWS_FT_FI2
Number of Residues56
DetailsBINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00198
ChainResidueDetails
AGLN33
BASP88
BGLU108
BASP140
BASP158
BPRO165
CGLN33
CHIS64
CASP88
CGLU108
CASP140
AHIS64
CASP158
CPRO165
DGLN33
DHIS64
DASP88
DGLU108
DASP140
DASP158
DPRO165
EGLN33
AASP88
EHIS64
EASP88
EGLU108
EASP140
EASP158
EPRO165
FGLN33
FHIS64
FASP88
FGLU108
AGLU108
FASP140
FASP158
FPRO165
GGLN33
GHIS64
GASP88
GGLU108
GASP140
GASP158
GPRO165
AASP140
HGLN33
HHIS64
HASP88
HGLU108
HASP140
HASP158
HPRO165
AASP158
APRO165
BGLN33
BHIS64

237735

PDB entries from 2025-06-18

PDB statisticsPDBj update infoContact PDBjnumon