Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6O65

Crystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 1 (AtSPDS1) in complex with decarboxylated S-adenosylmethionine and cyclohexylamine

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0004766	molecular_function	spermidine synthase activity
A	0005515	molecular_function	protein binding
A	0005829	cellular_component	cytosol
A	0006595	biological_process	polyamine metabolic process
A	0008295	biological_process	spermidine biosynthetic process
A	0016740	molecular_function	transferase activity
B	0003824	molecular_function	catalytic activity
B	0004766	molecular_function	spermidine synthase activity
B	0005515	molecular_function	protein binding
B	0005829	cellular_component	cytosol
B	0006595	biological_process	polyamine metabolic process
B	0008295	biological_process	spermidine biosynthetic process
B	0016740	molecular_function	transferase activity
C	0003824	molecular_function	catalytic activity
C	0004766	molecular_function	spermidine synthase activity
C	0005515	molecular_function	protein binding
C	0005829	cellular_component	cytosol
C	0006595	biological_process	polyamine metabolic process
C	0008295	biological_process	spermidine biosynthetic process
C	0016740	molecular_function	transferase activity
D	0003824	molecular_function	catalytic activity
D	0004766	molecular_function	spermidine synthase activity
D	0005515	molecular_function	protein binding
D	0005829	cellular_component	cytosol
D	0006595	biological_process	polyamine metabolic process
D	0008295	biological_process	spermidine biosynthetic process
D	0016740	molecular_function	transferase activity
E	0003824	molecular_function	catalytic activity
E	0004766	molecular_function	spermidine synthase activity
E	0005515	molecular_function	protein binding
E	0005829	cellular_component	cytosol
E	0006595	biological_process	polyamine metabolic process
E	0008295	biological_process	spermidine biosynthetic process
E	0016740	molecular_function	transferase activity
F	0003824	molecular_function	catalytic activity
F	0004766	molecular_function	spermidine synthase activity
F	0005515	molecular_function	protein binding
F	0005829	cellular_component	cytosol
F	0006595	biological_process	polyamine metabolic process
F	0008295	biological_process	spermidine biosynthetic process
F	0016740	molecular_function	transferase activity
G	0003824	molecular_function	catalytic activity
G	0004766	molecular_function	spermidine synthase activity
G	0005515	molecular_function	protein binding
G	0005829	cellular_component	cytosol
G	0006595	biological_process	polyamine metabolic process
G	0008295	biological_process	spermidine biosynthetic process
G	0016740	molecular_function	transferase activity
H	0003824	molecular_function	catalytic activity
H	0004766	molecular_function	spermidine synthase activity
H	0005515	molecular_function	protein binding
H	0005829	cellular_component	cytosol
H	0006595	biological_process	polyamine metabolic process
H	0008295	biological_process	spermidine biosynthetic process
H	0016740	molecular_function	transferase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	21
Details	binding site for residue S4M A 401

Chain	Residue
A	GLN76
A	ILE152
A	ASP153
A	VAL156
A	GLY181
A	ASP182
A	GLY183
A	ASP201
A	SER202
A	SER203
A	PRO208
A	LEU92
A	ALA209
A	TYR270
A	GLN97
A	TYR106
A	GLN107
A	GLY128
A	ASP131
A	CYS150
A	GLU151

site_id	AC2
Number of Residues	7
Details	binding site for residue HAI A 402

Chain	Residue
A	GLN97
A	ASP204
A	GLN234
A	TYR270
A	ILE275
A	HOH555
A	HOH564

site_id	AC3
Number of Residues	20
Details	binding site for residue S4M B 401

Chain	Residue
B	GLN76
B	GLN97
B	TYR106
B	GLY128
B	GLY129
B	GLY130
B	ASP131
B	CYS150
B	GLU151
B	ILE152
B	VAL156
B	ASP182
B	GLY183
B	ASP201
B	SER202
B	SER203
B	PRO208
B	ALA209
B	TYR270
B	HOH540

site_id	AC4
Number of Residues	7
Details	binding site for residue HAI B 402

Chain	Residue
B	VAL95
B	ILE96
B	GLN97
B	SER202
B	ASP204
B	HOH547
B	HOH590

site_id	AC5
Number of Residues	6
Details	binding site for residue SO4 B 403

Chain	Residue
B	LYS66
B	HOH576
B	HOH609
B	HOH629
B	HOH636
B	HOH644

site_id	AC6
Number of Residues	18
Details	binding site for residue S4M C 401

Chain	Residue
C	GLN76
C	GLN97
C	TYR106
C	GLN107
C	GLY128
C	ASP131
C	CYS150
C	GLU151
C	ILE152
C	VAL156
C	ASP182
C	GLY183
C	ASP201
C	SER202
C	SER203
C	PRO208
C	ALA209
C	TYR270

site_id	AC7
Number of Residues	7
Details	binding site for residue HAI C 402

Chain	Residue
C	GLN97
C	SER202
C	ASP204
C	GLN234
C	ILE275
C	HOH556
C	HOH557

site_id	AC8
Number of Residues	5
Details	binding site for residue SO4 C 403

Chain	Residue
C	ALA142
C	SER143
C	HOH506
C	HOH508
C	HOH589

site_id	AC9
Number of Residues	19
Details	binding site for residue S4M D 401

Chain	Residue
D	ILE152
D	VAL156
D	ASP182
D	GLY183
D	ASP201
D	SER202
D	SER203
D	PRO208
D	ALA209
D	LEU212
D	TYR270
D	GLN76
D	GLN97
D	TYR106
D	GLN107
D	GLY128
D	ASP131
D	CYS150
D	GLU151

site_id	AD1
Number of Residues	7
Details	binding site for residue HAI D 402

Chain	Residue
D	VAL95
D	ILE96
D	GLN97
D	ASP204
D	GLN234
D	HOH527
D	HOH541

site_id	AD2
Number of Residues	19
Details	binding site for residue S4M E 401

Chain	Residue
E	GLN76
E	GLN97
E	TYR106
E	GLN107
E	GLY128
E	ASP131
E	CYS150
E	GLU151
E	ILE152
E	ASP153
E	VAL156
E	ASP182
E	GLY183
E	ASP201
E	SER202
E	SER203
E	PRO208
E	ALA209
E	TYR270

site_id	AD3
Number of Residues	7
Details	binding site for residue HAI E 402

Chain	Residue
E	VAL95
E	ILE96
E	GLN97
E	SER202
E	ASP204
E	HOH1672
E	HOH1757

site_id	AD4
Number of Residues	8
Details	binding site for residue PEG E 403

Chain	Residue
E	MET54
E	TRP55
E	ASP204
E	PRO205
E	GLU236
E	HIS241
E	ILE244
E	HOH1718

site_id	AD5
Number of Residues	10
Details	binding site for residue SO4 E 404

Chain	Residue
E	ARG140
E	HIS141
E	ALA142
E	SER143
E	ASP297
E	HOH1698
E	HOH1715
E	HOH1740
E	HOH1741
E	HOH1766

site_id	AD6
Number of Residues	21
Details	binding site for residue S4M F 401

Chain	Residue
F	GLN76
F	LEU92
F	GLN97
F	TYR106
F	GLY128
F	ASP131
F	CYS150
F	GLU151
F	ILE152
F	ASP153
F	VAL156
F	ASP182
F	GLY183
F	ASP201
F	SER202
F	SER203
F	PRO208
F	ALA209
F	LEU212
F	TYR270
F	HOH614

site_id	AD7
Number of Residues	8
Details	binding site for residue HAI F 402

Chain	Residue
F	VAL95
F	GLN97
F	SER202
F	ASP204
F	GLN234
F	ILE275
F	HOH583
F	HOH637

site_id	AD8
Number of Residues	3
Details	binding site for residue EDO F 403

Chain	Residue
F	LYS72
F	SER73
F	ASP77

site_id	AD9
Number of Residues	19
Details	binding site for residue S4M G 401

Chain	Residue
G	GLN76
G	GLN97
G	TYR106
G	GLY128
G	ASP131
G	CYS150
G	GLU151
G	ILE152
G	ASP153
G	VAL156
G	ASP182
G	GLY183
G	ASP201
G	SER202
G	SER203
G	PRO208
G	ALA209
G	TYR270
G	HOH666

site_id	AE1
Number of Residues	9
Details	binding site for residue HAI G 402

Chain	Residue
G	VAL95
G	GLN97
G	SER202
G	ASP204
G	GLN234
G	TYR270
G	ILE275
G	HOH537
G	HOH555

site_id	AE2
Number of Residues	8
Details	binding site for residue PEG G 403

Chain	Residue
G	ASN261
G	LYS290
G	GLU330
G	HOH548
G	HOH557
G	HOH574
G	HOH609
G	HOH621

site_id	AE3
Number of Residues	3
Details	binding site for residue EDO G 404

Chain	Residue
G	ASN311
G	ALA312
G	HOH509

site_id	AE4
Number of Residues	7
Details	binding site for residue SO4 G 405

Chain	Residue
G	ARG140
G	HIS141
G	ALA142
G	SER143
G	ILE296
G	HOH584
G	HOH589

site_id	AE5
Number of Residues	20
Details	binding site for residue S4M H 401

Chain	Residue
H	GLN76
H	LEU92
H	GLN97
H	TYR106
H	GLY128
H	ASP131
H	CYS150
H	GLU151
H	ILE152
H	ASP153
H	VAL156
H	ASP182
H	GLY183
H	ASP201
H	SER202
H	SER203
H	PRO208
H	ALA209
H	TYR270
H	HOH532

site_id	AE6
Number of Residues	5
Details	binding site for residue HAI H 402

Chain	Residue
H	ASP204
H	GLN234
H	TYR270
H	HOH528
H	HOH584

Functional Information from PROSITE/UniProt

site_id	PS01330
Number of Residues	14
Details	PABS_1 Polyamine biosynthesis (PABS) domain signature. VLVIGGGdGgvLrE

Chain	Residue	Details
A	VAL124-GLU137

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	ACT_SITE: Proton acceptor => ECO:0000250

Chain	Residue	Details
A	ASP201
B	ASP201
C	ASP201
D	ASP201
E	ASP201
F	ASP201
G	ASP201
H	ASP201

site_id	SWS_FT_FI2
Number of Residues	64
Details	BINDING: BINDING => ECO:0000250

Chain	Residue	Details
A	GLN76
B	TYR106
B	GLN107
B	ASP131
B	GLU151
B	ASP182
B	ASP201
B	TYR270
C	GLN76
C	TYR106
C	GLN107
A	TYR106
C	ASP131
C	GLU151
C	ASP182
C	ASP201
C	TYR270
D	GLN76
D	TYR106
D	GLN107
D	ASP131
D	GLU151
A	GLN107
D	ASP182
D	ASP201
D	TYR270
E	GLN76
E	TYR106
E	GLN107
E	ASP131
E	GLU151
E	ASP182
E	ASP201
A	ASP131
E	TYR270
F	GLN76
F	TYR106
F	GLN107
F	ASP131
F	GLU151
F	ASP182
F	ASP201
F	TYR270
G	GLN76
A	GLU151
G	TYR106
G	GLN107
G	ASP131
G	GLU151
G	ASP182
G	ASP201
G	TYR270
H	GLN76
H	TYR106
H	GLN107
A	ASP182
H	ASP131
H	GLU151
H	ASP182
H	ASP201
H	TYR270
A	ASP201
A	TYR270
B	GLN76

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)