1GT8
DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, TERNARY COMPLEX WITH NADPH AND URACIL-4-ACETIC ACID
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0000166 | molecular_function | nucleotide binding |
A | 0002058 | molecular_function | uracil binding |
A | 0005737 | cellular_component | cytoplasm |
A | 0005829 | cellular_component | cytosol |
A | 0006210 | biological_process | thymine catabolic process |
A | 0006212 | biological_process | uracil catabolic process |
A | 0006214 | biological_process | thymidine catabolic process |
A | 0010181 | molecular_function | FMN binding |
A | 0016491 | molecular_function | oxidoreductase activity |
A | 0016627 | molecular_function | oxidoreductase activity, acting on the CH-CH group of donors |
A | 0017113 | molecular_function | dihydropyrimidine dehydrogenase (NADP+) activity |
A | 0019483 | biological_process | beta-alanine biosynthetic process |
A | 0042803 | molecular_function | protein homodimerization activity |
A | 0046872 | molecular_function | metal ion binding |
A | 0050660 | molecular_function | flavin adenine dinucleotide binding |
A | 0050661 | molecular_function | NADP binding |
A | 0051536 | molecular_function | iron-sulfur cluster binding |
A | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
B | 0000166 | molecular_function | nucleotide binding |
B | 0002058 | molecular_function | uracil binding |
B | 0005737 | cellular_component | cytoplasm |
B | 0005829 | cellular_component | cytosol |
B | 0006210 | biological_process | thymine catabolic process |
B | 0006212 | biological_process | uracil catabolic process |
B | 0006214 | biological_process | thymidine catabolic process |
B | 0010181 | molecular_function | FMN binding |
B | 0016491 | molecular_function | oxidoreductase activity |
B | 0016627 | molecular_function | oxidoreductase activity, acting on the CH-CH group of donors |
B | 0017113 | molecular_function | dihydropyrimidine dehydrogenase (NADP+) activity |
B | 0019483 | biological_process | beta-alanine biosynthetic process |
B | 0042803 | molecular_function | protein homodimerization activity |
B | 0046872 | molecular_function | metal ion binding |
B | 0050660 | molecular_function | flavin adenine dinucleotide binding |
B | 0050661 | molecular_function | NADP binding |
B | 0051536 | molecular_function | iron-sulfur cluster binding |
B | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
C | 0000166 | molecular_function | nucleotide binding |
C | 0002058 | molecular_function | uracil binding |
C | 0005737 | cellular_component | cytoplasm |
C | 0005829 | cellular_component | cytosol |
C | 0006210 | biological_process | thymine catabolic process |
C | 0006212 | biological_process | uracil catabolic process |
C | 0006214 | biological_process | thymidine catabolic process |
C | 0010181 | molecular_function | FMN binding |
C | 0016491 | molecular_function | oxidoreductase activity |
C | 0016627 | molecular_function | oxidoreductase activity, acting on the CH-CH group of donors |
C | 0017113 | molecular_function | dihydropyrimidine dehydrogenase (NADP+) activity |
C | 0019483 | biological_process | beta-alanine biosynthetic process |
C | 0042803 | molecular_function | protein homodimerization activity |
C | 0046872 | molecular_function | metal ion binding |
C | 0050660 | molecular_function | flavin adenine dinucleotide binding |
C | 0050661 | molecular_function | NADP binding |
C | 0051536 | molecular_function | iron-sulfur cluster binding |
C | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
D | 0000166 | molecular_function | nucleotide binding |
D | 0002058 | molecular_function | uracil binding |
D | 0005737 | cellular_component | cytoplasm |
D | 0005829 | cellular_component | cytosol |
D | 0006210 | biological_process | thymine catabolic process |
D | 0006212 | biological_process | uracil catabolic process |
D | 0006214 | biological_process | thymidine catabolic process |
D | 0010181 | molecular_function | FMN binding |
D | 0016491 | molecular_function | oxidoreductase activity |
D | 0016627 | molecular_function | oxidoreductase activity, acting on the CH-CH group of donors |
D | 0017113 | molecular_function | dihydropyrimidine dehydrogenase (NADP+) activity |
D | 0019483 | biological_process | beta-alanine biosynthetic process |
D | 0042803 | molecular_function | protein homodimerization activity |
D | 0046872 | molecular_function | metal ion binding |
D | 0050660 | molecular_function | flavin adenine dinucleotide binding |
D | 0050661 | molecular_function | NADP binding |
D | 0051536 | molecular_function | iron-sulfur cluster binding |
D | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE SF4 A1026 |
Chain | Residue |
A | CYS91 |
A | GLN156 |
A | PRO92 |
A | LEU95 |
A | ILE97 |
A | ASN120 |
A | CYS130 |
A | THR132 |
A | LEU135 |
A | CYS136 |
site_id | AC2 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE SF4 A1027 |
Chain | Residue |
A | CYS79 |
A | LEU80 |
A | LYS81 |
A | CYS82 |
A | PRO86 |
A | CYS87 |
A | CYS140 |
A | ASN141 |
A | ILE150 |
A | ILE152 |
site_id | AC3 |
Number of Residues | 12 |
Details | BINDING SITE FOR RESIDUE SF4 A1028 |
Chain | Residue |
A | ILE948 |
A | CYS953 |
A | ILE954 |
A | ASN955 |
A | CYS956 |
A | GLY957 |
A | LYS958 |
A | CYS959 |
A | CYS996 |
A | PRO997 |
A | CYS1001 |
A | ILE1002 |
site_id | AC4 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE SF4 A1029 |
Chain | Residue |
A | CYS963 |
A | TYR968 |
A | ILE971 |
A | VAL982 |
A | CYS986 |
A | THR987 |
A | GLY988 |
A | CYS989 |
A | THR990 |
A | CYS992 |
site_id | AC5 |
Number of Residues | 20 |
Details | BINDING SITE FOR RESIDUE FMN A1030 |
Chain | Residue |
A | ALA549 |
A | SER550 |
A | ALA551 |
A | LYS574 |
A | THR575 |
A | ILE590 |
A | ASN609 |
A | GLU611 |
A | ASN668 |
A | LYS709 |
A | THR737 |
A | SER766 |
A | GLY767 |
A | THR793 |
A | GLY794 |
A | GLY795 |
A | CYS816 |
A | SER817 |
A | GLN820 |
A | UAA1035 |
site_id | AC6 |
Number of Residues | 26 |
Details | BINDING SITE FOR RESIDUE FAD A1031 |
Chain | Residue |
A | VAL129 |
A | GLY194 |
A | GLY196 |
A | PRO197 |
A | ALA198 |
A | PHE217 |
A | GLU218 |
A | LYS219 |
A | GLN220 |
A | GLY225 |
A | LEU226 |
A | GLU230 |
A | ILE231 |
A | ARG235 |
A | SER260 |
A | LEU261 |
A | ILE283 |
A | LEU310 |
A | THR343 |
A | ASP346 |
A | GLY480 |
A | ASP481 |
A | THR488 |
A | THR489 |
A | SER492 |
A | NDP1032 |
site_id | AC7 |
Number of Residues | 13 |
Details | BINDING SITE FOR RESIDUE NDP A1032 |
Chain | Residue |
A | ASN487 |
A | FAD1031 |
A | PRO131 |
A | ALA340 |
A | GLY341 |
A | ASP342 |
A | THR343 |
A | ARG364 |
A | LYS365 |
A | ARG371 |
A | ALA437 |
A | PHE438 |
A | GLY439 |
site_id | AC8 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE UAA A1035 |
Chain | Residue |
A | ASN609 |
A | GLU611 |
A | LEU612 |
A | ILE613 |
A | ASN668 |
A | SER670 |
A | ASN736 |
A | GLY764 |
A | FMN1030 |
site_id | AC9 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE SF4 B1026 |
Chain | Residue |
B | CYS91 |
B | PRO92 |
B | LEU95 |
B | ILE97 |
B | ASN120 |
B | CYS130 |
B | THR132 |
B | CYS136 |
B | GLN156 |
site_id | BC1 |
Number of Residues | 11 |
Details | BINDING SITE FOR RESIDUE SF4 B1027 |
Chain | Residue |
B | CYS79 |
B | LEU80 |
B | LYS81 |
B | CYS82 |
B | PRO86 |
B | CYS87 |
B | CYS140 |
B | ASN141 |
B | LEU142 |
B | ILE150 |
B | ILE152 |
site_id | BC2 |
Number of Residues | 11 |
Details | BINDING SITE FOR RESIDUE SF4 B1028 |
Chain | Residue |
B | ILE948 |
B | CYS953 |
B | ILE954 |
B | CYS956 |
B | GLY957 |
B | LYS958 |
B | CYS959 |
B | CYS996 |
B | PRO997 |
B | CYS1001 |
B | ILE1002 |
site_id | BC3 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE SF4 B1029 |
Chain | Residue |
B | CYS963 |
B | TYR968 |
B | ILE971 |
B | VAL982 |
B | CYS986 |
B | THR987 |
B | GLY988 |
B | CYS989 |
B | THR990 |
B | CYS992 |
site_id | BC4 |
Number of Residues | 21 |
Details | BINDING SITE FOR RESIDUE FMN B1030 |
Chain | Residue |
B | ALA549 |
B | SER550 |
B | ALA551 |
B | LYS574 |
B | THR575 |
B | ILE590 |
B | ASN609 |
B | ASN668 |
B | LYS709 |
B | THR735 |
B | ASN736 |
B | THR737 |
B | SER766 |
B | GLY767 |
B | THR793 |
B | GLY794 |
B | GLY795 |
B | CYS816 |
B | SER817 |
B | GLN820 |
B | UAA1035 |
site_id | BC5 |
Number of Residues | 27 |
Details | BINDING SITE FOR RESIDUE FAD B1031 |
Chain | Residue |
B | VAL129 |
B | GLY194 |
B | GLY196 |
B | PRO197 |
B | ALA198 |
B | PHE217 |
B | GLU218 |
B | LYS219 |
B | GLN220 |
B | GLY225 |
B | LEU226 |
B | GLU230 |
B | ILE231 |
B | ARG235 |
B | LYS259 |
B | SER260 |
B | LEU261 |
B | ILE283 |
B | LEU310 |
B | THR343 |
B | ASP346 |
B | GLY480 |
B | ASP481 |
B | THR488 |
B | THR489 |
B | SER492 |
B | NDP1032 |
site_id | BC6 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE NDP B1032 |
Chain | Residue |
B | PRO131 |
B | ALA340 |
B | GLY341 |
B | ASP342 |
B | THR343 |
B | ARG364 |
B | LYS365 |
B | ARG371 |
B | PRO393 |
B | ALA437 |
B | PHE438 |
B | GLY439 |
B | ASN487 |
B | FAD1031 |
site_id | BC7 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE UAA B1035 |
Chain | Residue |
B | ASN609 |
B | GLU611 |
B | ILE613 |
B | ASN668 |
B | SER670 |
B | ASN736 |
B | THR737 |
B | GLY764 |
B | FMN1030 |
site_id | BC8 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE SF4 C1026 |
Chain | Residue |
C | CYS91 |
C | PRO92 |
C | LEU95 |
C | ILE97 |
C | CYS130 |
C | THR132 |
C | LEU135 |
C | CYS136 |
C | GLN156 |
site_id | BC9 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE SF4 C1027 |
Chain | Residue |
C | CYS79 |
C | LEU80 |
C | LYS81 |
C | CYS82 |
C | CYS87 |
C | CYS140 |
C | ASN141 |
C | ILE150 |
C | ILE152 |
site_id | CC1 |
Number of Residues | 11 |
Details | BINDING SITE FOR RESIDUE SF4 C1028 |
Chain | Residue |
C | ILE948 |
C | CYS953 |
C | ILE954 |
C | CYS956 |
C | GLY957 |
C | LYS958 |
C | CYS959 |
C | CYS996 |
C | PRO997 |
C | CYS1001 |
C | ILE1002 |
site_id | CC2 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE SF4 C1029 |
Chain | Residue |
C | CYS963 |
C | TYR968 |
C | ILE971 |
C | VAL982 |
C | CYS986 |
C | THR987 |
C | GLY988 |
C | CYS989 |
C | THR990 |
C | CYS992 |
site_id | CC3 |
Number of Residues | 19 |
Details | BINDING SITE FOR RESIDUE FMN C1030 |
Chain | Residue |
C | ALA549 |
C | SER550 |
C | ALA551 |
C | LYS574 |
C | THR575 |
C | ILE590 |
C | ASN609 |
C | ASN668 |
C | LYS709 |
C | ASN736 |
C | SER766 |
C | GLY767 |
C | THR793 |
C | GLY794 |
C | GLY795 |
C | CYS816 |
C | SER817 |
C | GLN820 |
C | UAA1035 |
site_id | CC4 |
Number of Residues | 27 |
Details | BINDING SITE FOR RESIDUE FAD C1031 |
Chain | Residue |
C | VAL129 |
C | GLY194 |
C | GLY196 |
C | PRO197 |
C | ALA198 |
C | PHE217 |
C | GLU218 |
C | LYS219 |
C | GLN220 |
C | GLY225 |
C | LEU226 |
C | GLU230 |
C | ILE231 |
C | ARG235 |
C | SER260 |
C | LEU261 |
C | GLY282 |
C | ILE283 |
C | LEU310 |
C | THR343 |
C | ASP346 |
C | GLY480 |
C | ASP481 |
C | THR488 |
C | THR489 |
C | SER492 |
C | NDP1032 |
site_id | CC5 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE NDP C1032 |
Chain | Residue |
C | PRO131 |
C | ALA340 |
C | GLY341 |
C | ASP342 |
C | THR343 |
C | ARG364 |
C | LYS365 |
C | ARG371 |
C | ALA437 |
C | PHE438 |
C | GLY439 |
C | ASN487 |
C | THR488 |
C | FAD1031 |
site_id | CC6 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE UAA C1035 |
Chain | Residue |
C | ASN609 |
C | GLU611 |
C | LEU612 |
C | ILE613 |
C | ASN668 |
C | SER670 |
C | ASN736 |
C | THR737 |
C | GLY764 |
C | FMN1030 |
site_id | CC7 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE SF4 D1026 |
Chain | Residue |
D | CYS91 |
D | PRO92 |
D | LEU95 |
D | ILE97 |
D | ASN120 |
D | CYS130 |
D | THR132 |
D | CYS136 |
D | GLN156 |
site_id | CC8 |
Number of Residues | 11 |
Details | BINDING SITE FOR RESIDUE SF4 D1027 |
Chain | Residue |
D | CYS79 |
D | LEU80 |
D | LYS81 |
D | CYS82 |
D | PRO86 |
D | CYS87 |
D | CYS140 |
D | ASN141 |
D | LEU142 |
D | ILE150 |
D | ILE152 |
site_id | CC9 |
Number of Residues | 11 |
Details | BINDING SITE FOR RESIDUE SF4 D1028 |
Chain | Residue |
D | ILE948 |
D | CYS953 |
D | ILE954 |
D | CYS956 |
D | GLY957 |
D | LYS958 |
D | CYS959 |
D | CYS996 |
D | PRO997 |
D | CYS1001 |
D | ILE1002 |
site_id | DC1 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE SF4 D1029 |
Chain | Residue |
D | CYS963 |
D | TYR968 |
D | ILE971 |
D | VAL982 |
D | CYS986 |
D | THR987 |
D | GLY988 |
D | CYS989 |
D | THR990 |
D | CYS992 |
site_id | DC2 |
Number of Residues | 20 |
Details | BINDING SITE FOR RESIDUE FMN D1030 |
Chain | Residue |
D | ALA549 |
D | SER550 |
D | ALA551 |
D | LYS574 |
D | THR575 |
D | ILE590 |
D | ASN609 |
D | ASN668 |
D | LYS709 |
D | THR735 |
D | THR737 |
D | SER766 |
D | GLY767 |
D | THR793 |
D | GLY794 |
D | GLY795 |
D | CYS816 |
D | SER817 |
D | GLN820 |
D | UAA1035 |
site_id | DC3 |
Number of Residues | 27 |
Details | BINDING SITE FOR RESIDUE FAD D1031 |
Chain | Residue |
D | VAL129 |
D | GLY194 |
D | GLY196 |
D | PRO197 |
D | ALA198 |
D | PHE217 |
D | GLU218 |
D | LYS219 |
D | GLN220 |
D | GLY225 |
D | LEU226 |
D | GLU230 |
D | ILE231 |
D | ARG235 |
D | LYS259 |
D | SER260 |
D | LEU261 |
D | ILE283 |
D | LEU310 |
D | THR343 |
D | ASP346 |
D | GLY480 |
D | ASP481 |
D | THR488 |
D | THR489 |
D | SER492 |
D | NDP1032 |
site_id | DC4 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE NDP D1032 |
Chain | Residue |
D | PRO131 |
D | ALA340 |
D | GLY341 |
D | ASP342 |
D | THR343 |
D | ARG364 |
D | LYS365 |
D | ARG371 |
D | PRO393 |
D | ALA437 |
D | PHE438 |
D | GLY439 |
D | ASN487 |
D | THR488 |
D | FAD1031 |
site_id | DC5 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE UAA D1035 |
Chain | Residue |
D | ASN609 |
D | GLU611 |
D | ILE613 |
D | ASN668 |
D | ASN736 |
D | THR737 |
D | FMN1030 |
Functional Information from PROSITE/UniProt
site_id | PS00198 |
Number of Residues | 12 |
Details | 4FE4S_FER_1 4Fe-4S ferredoxin-type iron-sulfur binding region signature. CtGCTlCLsVCP |
Chain | Residue | Details |
A | CYS986-PRO997 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 4 |
Details | ACT_SITE: Proton acceptor => ECO:0000269|PubMed:11796730 |
Chain | Residue | Details |
A | CYS671 | |
B | CYS671 | |
C | CYS671 | |
D | CYS671 |
site_id | SWS_FT_FI2 |
Number of Residues | 76 |
Details | BINDING: |
Chain | Residue | Details |
A | CYS79 | |
A | ASN668 | |
A | ASN736 | |
A | CYS953 | |
A | CYS956 | |
A | CYS959 | |
A | CYS963 | |
A | CYS986 | |
A | CYS989 | |
A | CYS992 | |
A | CYS996 | |
A | CYS82 | |
B | CYS79 | |
B | CYS82 | |
B | CYS87 | |
B | CYS91 | |
B | CYS130 | |
B | CYS136 | |
B | CYS140 | |
B | GLN156 | |
B | ASN609 | |
B | ASN668 | |
A | CYS87 | |
B | ASN736 | |
B | CYS953 | |
B | CYS956 | |
B | CYS959 | |
B | CYS963 | |
B | CYS986 | |
B | CYS989 | |
B | CYS992 | |
B | CYS996 | |
C | CYS79 | |
A | CYS91 | |
C | CYS82 | |
C | CYS87 | |
C | CYS91 | |
C | CYS130 | |
C | CYS136 | |
C | CYS140 | |
C | GLN156 | |
C | ASN609 | |
C | ASN668 | |
C | ASN736 | |
A | CYS130 | |
C | CYS953 | |
C | CYS956 | |
C | CYS959 | |
C | CYS963 | |
C | CYS986 | |
C | CYS989 | |
C | CYS992 | |
C | CYS996 | |
D | CYS79 | |
D | CYS82 | |
A | CYS136 | |
D | CYS87 | |
D | CYS91 | |
D | CYS130 | |
D | CYS136 | |
D | CYS140 | |
D | GLN156 | |
D | ASN609 | |
D | ASN668 | |
D | ASN736 | |
D | CYS953 | |
A | CYS140 | |
D | CYS956 | |
D | CYS959 | |
D | CYS963 | |
D | CYS986 | |
D | CYS989 | |
D | CYS992 | |
D | CYS996 | |
A | GLN156 | |
A | ASN609 |
site_id | SWS_FT_FI3 |
Number of Residues | 68 |
Details | BINDING: BINDING => ECO:0000269|PubMed:11796730 |
Chain | Residue | Details |
A | VAL129 | |
A | GLY480 | |
A | ASP481 | |
A | SER550 | |
A | LYS574 | |
A | LYS709 | |
A | GLY767 | |
A | THR793 | |
A | CYS816 | |
B | VAL129 | |
B | GLY194 | |
A | GLY194 | |
B | GLU218 | |
B | ARG235 | |
B | LEU261 | |
B | ALA340 | |
B | ARG364 | |
B | ARG371 | |
B | ALA437 | |
B | GLY480 | |
B | ASP481 | |
B | SER550 | |
A | GLU218 | |
B | LYS574 | |
B | LYS709 | |
B | GLY767 | |
B | THR793 | |
B | CYS816 | |
C | VAL129 | |
C | GLY194 | |
C | GLU218 | |
C | ARG235 | |
C | LEU261 | |
A | ARG235 | |
C | ALA340 | |
C | ARG364 | |
C | ARG371 | |
C | ALA437 | |
C | GLY480 | |
C | ASP481 | |
C | SER550 | |
C | LYS574 | |
C | LYS709 | |
C | GLY767 | |
A | LEU261 | |
C | THR793 | |
C | CYS816 | |
D | VAL129 | |
D | GLY194 | |
D | GLU218 | |
D | ARG235 | |
D | LEU261 | |
D | ALA340 | |
D | ARG364 | |
D | ARG371 | |
A | ALA340 | |
D | ALA437 | |
D | GLY480 | |
D | ASP481 | |
D | SER550 | |
D | LYS574 | |
D | LYS709 | |
D | GLY767 | |
D | THR793 | |
D | CYS816 | |
A | ARG364 | |
A | ARG371 | |
A | ALA437 |
site_id | SWS_FT_FI4 |
Number of Residues | 4 |
Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q12882 |
Chain | Residue | Details |
A | LYS384 | |
B | LYS384 | |
C | LYS384 | |
D | LYS384 |
Catalytic Information from CSA
site_id | MCSA1 |
Number of Residues | 3 |
Details | M-CSA 800 |
Chain | Residue | Details |
A | LYS574 | electrostatic stabiliser |
A | CYS671 | proton acceptor, proton donor |
A | LYS709 | electrostatic stabiliser |
site_id | MCSA2 |
Number of Residues | 3 |
Details | M-CSA 800 |
Chain | Residue | Details |
B | LYS574 | electrostatic stabiliser |
B | CYS671 | proton acceptor, proton donor |
B | LYS709 | electrostatic stabiliser |
site_id | MCSA3 |
Number of Residues | 3 |
Details | M-CSA 800 |
Chain | Residue | Details |
C | LYS574 | electrostatic stabiliser |
C | CYS671 | proton acceptor, proton donor |
C | LYS709 | electrostatic stabiliser |
site_id | MCSA4 |
Number of Residues | 3 |
Details | M-CSA 800 |
Chain | Residue | Details |
D | LYS574 | electrostatic stabiliser |
D | CYS671 | proton acceptor, proton donor |
D | LYS709 | electrostatic stabiliser |