3HRD
Crystal structure of nicotinate dehydrogenase
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0005506 | molecular_function | iron ion binding |
A | 0016491 | molecular_function | oxidoreductase activity |
A | 0046872 | molecular_function | metal ion binding |
A | 0050138 | molecular_function | nicotinate dehydrogenase activity |
A | 1901848 | biological_process | nicotinate catabolic process |
B | 0016491 | molecular_function | oxidoreductase activity |
B | 0046872 | molecular_function | metal ion binding |
B | 0050138 | molecular_function | nicotinate dehydrogenase activity |
B | 1901848 | biological_process | nicotinate catabolic process |
C | 0016491 | molecular_function | oxidoreductase activity |
C | 0050138 | molecular_function | nicotinate dehydrogenase activity |
C | 0050660 | molecular_function | flavin adenine dinucleotide binding |
C | 0071949 | molecular_function | FAD binding |
C | 1901848 | biological_process | nicotinate catabolic process |
D | 0000166 | molecular_function | nucleotide binding |
D | 0016491 | molecular_function | oxidoreductase activity |
D | 0046872 | molecular_function | metal ion binding |
D | 0050138 | molecular_function | nicotinate dehydrogenase activity |
D | 0051536 | molecular_function | iron-sulfur cluster binding |
D | 0051537 | molecular_function | 2 iron, 2 sulfur cluster binding |
D | 1901848 | biological_process | nicotinate catabolic process |
E | 0005506 | molecular_function | iron ion binding |
E | 0016491 | molecular_function | oxidoreductase activity |
E | 0046872 | molecular_function | metal ion binding |
E | 0050138 | molecular_function | nicotinate dehydrogenase activity |
E | 1901848 | biological_process | nicotinate catabolic process |
F | 0016491 | molecular_function | oxidoreductase activity |
F | 0046872 | molecular_function | metal ion binding |
F | 0050138 | molecular_function | nicotinate dehydrogenase activity |
F | 1901848 | biological_process | nicotinate catabolic process |
G | 0016491 | molecular_function | oxidoreductase activity |
G | 0050138 | molecular_function | nicotinate dehydrogenase activity |
G | 0050660 | molecular_function | flavin adenine dinucleotide binding |
G | 0071949 | molecular_function | FAD binding |
G | 1901848 | biological_process | nicotinate catabolic process |
H | 0000166 | molecular_function | nucleotide binding |
H | 0016491 | molecular_function | oxidoreductase activity |
H | 0046872 | molecular_function | metal ion binding |
H | 0050138 | molecular_function | nicotinate dehydrogenase activity |
H | 0051536 | molecular_function | iron-sulfur cluster binding |
H | 0051537 | molecular_function | 2 iron, 2 sulfur cluster binding |
H | 1901848 | biological_process | nicotinate catabolic process |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE SE A 922 |
Chain | Residue |
A | PHE239 |
A | GLY240 |
A | ALA349 |
A | PHE350 |
A | ARG351 |
B | GLU289 |
B | MOS920 |
B | MCN921 |
site_id | AC2 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE NO3 A 5658 |
Chain | Residue |
A | HIS279 |
A | VAL316 |
A | GLY348 |
A | ALA349 |
A | PHE350 |
A | PHE353 |
A | GLY354 |
A | GLN357 |
A | ARG278 |
site_id | AC3 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE MG A 426 |
Chain | Residue |
A | THR207 |
A | ASN209 |
A | ASP213 |
A | LYS242 |
A | LEU243 |
A | ASP244 |
A | GLN248 |
A | HOH448 |
site_id | AC4 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MG A 427 |
Chain | Residue |
A | THR306 |
A | TYR309 |
A | ALA310 |
A | SER347 |
site_id | AC5 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE MOS B 920 |
Chain | Residue |
A | GLN208 |
A | GLY240 |
A | LEU243 |
A | PHE353 |
A | SE922 |
B | THR84 |
B | SER85 |
B | ALA86 |
B | GLU289 |
B | MCN921 |
site_id | AC6 |
Number of Residues | 35 |
Details | BINDING SITE FOR RESIDUE MCN B 921 |
Chain | Residue |
A | GLY237 |
A | GLY238 |
A | PHE239 |
A | ARG351 |
A | SE922 |
B | ILE45 |
B | GLY46 |
B | GLN47 |
B | GLY48 |
B | SER49 |
B | THR84 |
B | SER85 |
B | ALA86 |
B | SER87 |
B | ARG88 |
B | GLN89 |
B | THR90 |
B | VAL211 |
B | THR213 |
B | ILE215 |
B | ASN216 |
B | MET219 |
B | VAL220 |
B | GLN223 |
B | ALA284 |
B | LYS285 |
B | GLY286 |
B | VAL287 |
B | GLY288 |
B | GLU289 |
B | HOH384 |
B | HOH446 |
B | MOS920 |
D | GLN100 |
D | CYS138 |
site_id | AC7 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE NIO B 5661 |
Chain | Residue |
A | TYR312 |
A | ALA315 |
A | ARG319 |
A | PHE353 |
A | HOH513 |
B | ASN17 |
B | THR18 |
B | LEU20 |
site_id | AC8 |
Number of Residues | 33 |
Details | BINDING SITE FOR RESIDUE FAD C 900 |
Chain | Residue |
C | THR117 |
C | GLY122 |
C | ASP123 |
C | ARG160 |
C | ILE168 |
C | MET169 |
C | LYS187 |
C | ALA195 |
C | HOH303 |
C | HOH329 |
C | HOH359 |
C | HOH361 |
C | HOH388 |
D | GLU44 |
D | GLY45 |
D | GLU46 |
C | ILE29 |
C | ALA31 |
C | GLY32 |
C | GLY33 |
C | THR34 |
C | ASP35 |
C | LEU36 |
C | ILE38 |
C | ALA73 |
C | PHE77 |
C | VAL100 |
C | GLY101 |
C | ILE105 |
C | THR110 |
C | GLY113 |
C | ASN114 |
C | SER116 |
site_id | AC9 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE NO3 C 5659 |
Chain | Residue |
C | CYS222 |
C | ARG265 |
C | PRO266 |
C | SER267 |
C | VAL268 |
C | LYS271 |
site_id | BC1 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE FES D 907 |
Chain | Residue |
A | ILE186 |
D | GLN100 |
D | CYS101 |
D | GLY102 |
D | CYS104 |
D | CYS136 |
D | ARG137 |
D | CYS138 |
site_id | BC2 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE FES D 908 |
Chain | Residue |
D | GLY41 |
D | CYS42 |
D | SER43 |
D | GLY45 |
D | GLU46 |
D | CYS47 |
D | GLY48 |
D | CYS50 |
D | THR60 |
D | CYS62 |
site_id | BC3 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE SE E 922 |
Chain | Residue |
E | PHE239 |
E | GLY240 |
E | ALA349 |
E | PHE350 |
E | ARG351 |
F | GLU289 |
F | MOS920 |
F | MCN921 |
site_id | BC4 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE NIO E 5660 |
Chain | Residue |
A | GLU198 |
E | VAL15 |
E | GLU19 |
E | HOH441 |
E | HOH757 |
F | VAL70 |
F | THR71 |
F | TRP72 |
site_id | BC5 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE NO3 E 5662 |
Chain | Residue |
E | ARG278 |
E | HIS279 |
E | VAL316 |
E | GLY348 |
E | ALA349 |
E | PHE350 |
E | GLY354 |
E | GLN357 |
site_id | BC6 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE CA E 5663 |
Chain | Residue |
E | THR207 |
E | ASN209 |
E | ASP213 |
E | LYS242 |
E | LEU243 |
E | ASP244 |
E | GLN248 |
site_id | BC7 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE MOS F 920 |
Chain | Residue |
E | GLN208 |
E | GLY240 |
E | LEU243 |
E | SE922 |
F | THR84 |
F | SER85 |
F | ALA86 |
F | GLU289 |
F | MCN921 |
site_id | BC8 |
Number of Residues | 34 |
Details | BINDING SITE FOR RESIDUE MCN F 921 |
Chain | Residue |
E | GLY238 |
E | PHE239 |
E | ARG351 |
E | SE922 |
F | ILE45 |
F | GLY46 |
F | GLN47 |
F | GLY48 |
F | SER49 |
F | THR84 |
F | SER85 |
F | ALA86 |
F | SER87 |
F | ARG88 |
F | GLN89 |
F | THR90 |
F | VAL211 |
F | THR213 |
F | ILE215 |
F | ASN216 |
F | MET219 |
F | VAL220 |
F | GLN223 |
F | ALA284 |
F | LYS285 |
F | GLY286 |
F | VAL287 |
F | GLY288 |
F | GLU289 |
F | HOH333 |
F | HOH895 |
F | MOS920 |
H | GLN100 |
H | CYS138 |
site_id | BC9 |
Number of Residues | 29 |
Details | BINDING SITE FOR RESIDUE FAD G 900 |
Chain | Residue |
G | ILE29 |
G | ALA31 |
G | GLY32 |
G | GLY33 |
G | THR34 |
G | ASP35 |
G | LEU36 |
G | ILE38 |
G | ILE53 |
G | PHE77 |
G | VAL100 |
G | GLY101 |
G | ILE105 |
G | THR110 |
G | GLY113 |
G | ASN114 |
G | SER116 |
G | THR117 |
G | GLY122 |
G | ASP123 |
G | ARG160 |
G | ILE168 |
G | MET169 |
G | LYS187 |
G | ALA195 |
G | HOH297 |
H | GLU44 |
H | GLY45 |
H | GLU46 |
site_id | CC1 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE FES H 907 |
Chain | Residue |
E | ILE186 |
H | GLN100 |
H | CYS101 |
H | GLY102 |
H | CYS104 |
H | CYS136 |
H | ARG137 |
H | CYS138 |
site_id | CC2 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE FES H 908 |
Chain | Residue |
H | GLY41 |
H | CYS42 |
H | SER43 |
H | GLY45 |
H | GLU46 |
H | CYS47 |
H | GLY48 |
H | CYS50 |
H | CYS62 |
Functional Information from PROSITE/UniProt
site_id | PS00197 |
Number of Residues | 9 |
Details | 2FE2S_FER_1 2Fe-2S ferredoxin-type iron-sulfur binding region signature. CSEGECGAC |
Chain | Residue | Details |
D | CYS42-CYS50 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 16 |
Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00465, ECO:0000269|PubMed:19549881 |
Chain | Residue | Details |
D | CYS42 | |
H | CYS47 | |
H | CYS50 | |
H | CYS62 | |
H | CYS101 | |
H | CYS104 | |
H | CYS136 | |
H | CYS138 | |
D | CYS47 | |
D | CYS50 | |
D | CYS62 | |
D | CYS101 | |
D | CYS104 | |
D | CYS136 | |
D | CYS138 | |
H | CYS42 |
site_id | SWS_FT_FI2 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0000269|PubMed:19549881 |
Chain | Residue | Details |
B | ILE45 | |
B | SER85 | |
B | VAL211 | |
B | ALA284 | |
F | ILE45 | |
F | SER85 | |
F | VAL211 | |
F | ALA284 |
Catalytic Information from CSA
site_id | CSA1 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1fiq |
Chain | Residue | Details |
A | GLN208 | |
A | ARG351 |
site_id | CSA2 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1fiq |
Chain | Residue | Details |
E | GLN208 | |
E | ARG351 |
site_id | CSA3 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1fiq |
Chain | Residue | Details |
B | GLU289 |
site_id | CSA4 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1fiq |
Chain | Residue | Details |
F | GLU289 |