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 |