1V59
Crystal structure of yeast lipoamide dehydrogenase complexed with NAD+
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0004148 | molecular_function | dihydrolipoyl dehydrogenase activity |
A | 0004375 | molecular_function | glycine dehydrogenase (decarboxylating) activity |
A | 0004591 | molecular_function | oxoglutarate dehydrogenase (succinyl-transferring) activity |
A | 0004738 | molecular_function | pyruvate dehydrogenase activity |
A | 0005515 | molecular_function | protein binding |
A | 0005739 | cellular_component | mitochondrion |
A | 0005759 | cellular_component | mitochondrial matrix |
A | 0005960 | cellular_component | glycine cleavage complex |
A | 0006086 | biological_process | acetyl-CoA biosynthetic process from pyruvate |
A | 0006090 | biological_process | pyruvate metabolic process |
A | 0006099 | biological_process | tricarboxylic acid cycle |
A | 0006103 | biological_process | 2-oxoglutarate metabolic process |
A | 0006546 | biological_process | glycine catabolic process |
A | 0006550 | biological_process | isoleucine catabolic process |
A | 0006552 | biological_process | L-leucine catabolic process |
A | 0006564 | biological_process | L-serine biosynthetic process |
A | 0006574 | biological_process | valine catabolic process |
A | 0016491 | molecular_function | oxidoreductase activity |
A | 0016668 | molecular_function | oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor |
A | 0042645 | cellular_component | mitochondrial nucleoid |
A | 0042743 | biological_process | hydrogen peroxide metabolic process |
A | 0045252 | cellular_component | oxoglutarate dehydrogenase complex |
A | 0045254 | cellular_component | pyruvate dehydrogenase complex |
A | 0050660 | molecular_function | flavin adenine dinucleotide binding |
B | 0004148 | molecular_function | dihydrolipoyl dehydrogenase activity |
B | 0004375 | molecular_function | glycine dehydrogenase (decarboxylating) activity |
B | 0004591 | molecular_function | oxoglutarate dehydrogenase (succinyl-transferring) activity |
B | 0004738 | molecular_function | pyruvate dehydrogenase activity |
B | 0005515 | molecular_function | protein binding |
B | 0005739 | cellular_component | mitochondrion |
B | 0005759 | cellular_component | mitochondrial matrix |
B | 0005960 | cellular_component | glycine cleavage complex |
B | 0006086 | biological_process | acetyl-CoA biosynthetic process from pyruvate |
B | 0006090 | biological_process | pyruvate metabolic process |
B | 0006099 | biological_process | tricarboxylic acid cycle |
B | 0006103 | biological_process | 2-oxoglutarate metabolic process |
B | 0006546 | biological_process | glycine catabolic process |
B | 0006550 | biological_process | isoleucine catabolic process |
B | 0006552 | biological_process | L-leucine catabolic process |
B | 0006564 | biological_process | L-serine biosynthetic process |
B | 0006574 | biological_process | valine catabolic process |
B | 0016491 | molecular_function | oxidoreductase activity |
B | 0016668 | molecular_function | oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor |
B | 0042645 | cellular_component | mitochondrial nucleoid |
B | 0042743 | biological_process | hydrogen peroxide metabolic process |
B | 0045252 | cellular_component | oxoglutarate dehydrogenase complex |
B | 0045254 | cellular_component | pyruvate dehydrogenase complex |
B | 0050660 | molecular_function | flavin adenine dinucleotide binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE PO4 A 484 |
Chain | Residue |
A | ILE2 |
A | VAL138 |
A | LYS139 |
A | GLU140 |
A | HIS142 |
site_id | AC2 |
Number of Residues | 37 |
Details | BINDING SITE FOR RESIDUE FAD A 480 |
Chain | Residue |
A | VAL34 |
A | GLU35 |
A | LYS36 |
A | ARG37 |
A | GLY42 |
A | THR43 |
A | CYS44 |
A | GLY48 |
A | CYS49 |
A | LYS53 |
A | GLY116 |
A | ASN117 |
A | GLY118 |
A | ALA152 |
A | THR153 |
A | GLY154 |
A | SER155 |
A | SER173 |
A | ARG285 |
A | TYR288 |
A | GLY324 |
A | ASP325 |
A | MET331 |
A | LEU332 |
A | ALA333 |
A | HIS334 |
A | TYR364 |
A | HOH579 |
A | HOH580 |
A | HOH581 |
A | HOH612 |
A | HOH658 |
B | HIS457 |
A | GLY12 |
A | GLY14 |
A | PRO15 |
A | ALA16 |
site_id | AC3 |
Number of Residues | 35 |
Details | BINDING SITE FOR RESIDUE FAD B 481 |
Chain | Residue |
A | HIS457 |
B | GLY12 |
B | GLY14 |
B | PRO15 |
B | ALA16 |
B | GLU35 |
B | LYS36 |
B | ARG37 |
B | GLY42 |
B | THR43 |
B | CYS44 |
B | GLY48 |
B | CYS49 |
B | LYS53 |
B | GLY116 |
B | ASN117 |
B | GLY118 |
B | ALA152 |
B | THR153 |
B | GLY154 |
B | SER155 |
B | ARG285 |
B | TYR288 |
B | GLY324 |
B | ASP325 |
B | MET331 |
B | LEU332 |
B | ALA333 |
B | HIS334 |
B | TYR364 |
B | HOH500 |
B | HOH504 |
B | HOH530 |
B | HOH573 |
B | HOH809 |
site_id | AC4 |
Number of Residues | 13 |
Details | BINDING SITE FOR RESIDUE NAD A 482 |
Chain | Residue |
A | PHE160 |
A | GLY190 |
A | GLY192 |
A | GLU213 |
A | PHE214 |
A | GLN215 |
A | THR245 |
A | LYS246 |
A | VAL247 |
A | ALA282 |
A | VAL283 |
A | GLY284 |
A | HOH829 |
site_id | AC5 |
Number of Residues | 12 |
Details | BINDING SITE FOR RESIDUE NAD B 483 |
Chain | Residue |
B | VAL283 |
B | GLY284 |
B | HOH563 |
B | PHE160 |
B | ILE189 |
B | GLY190 |
B | VAL212 |
B | GLU213 |
B | PHE214 |
B | GLN215 |
B | THR245 |
B | VAL247 |
Functional Information from PROSITE/UniProt
site_id | PS00076 |
Number of Residues | 11 |
Details | PYRIDINE_REDOX_1 Pyridine nucleotide-disulphide oxidoreductases class-I active site. GGtCLnvGCIP |
Chain | Residue | Details |
A | GLY41-PRO51 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 2 |
Details | ACT_SITE: Proton acceptor => ECO:0000269|PubMed:9538259 |
Chain | Residue | Details |
A | HIS457 | |
B | HIS457 |
site_id | SWS_FT_FI2 |
Number of Residues | 10 |
Details | BINDING: BINDING => ECO:0000269|PubMed:9538259, ECO:0000269|Ref.13 |
Chain | Residue | Details |
A | GLU35 | |
B | MET331 | |
A | LYS53 | |
A | GLY118 | |
A | ASP325 | |
A | MET331 | |
B | GLU35 | |
B | LYS53 | |
B | GLY118 | |
B | ASP325 |
site_id | SWS_FT_FI3 |
Number of Residues | 10 |
Details | BINDING: BINDING => ECO:0000250 |
Chain | Residue | Details |
A | THR153 | |
B | GLY284 | |
A | GLY190 | |
A | GLU213 | |
A | VAL247 | |
A | GLY284 | |
B | THR153 | |
B | GLY190 | |
B | GLU213 | |
B | VAL247 |
Catalytic Information from CSA
site_id | CSA1 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1get |
Chain | Residue | Details |
A | GLU462 | |
A | HIS457 |
site_id | CSA2 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1get |
Chain | Residue | Details |
B | GLU462 | |
B | HIS457 |
site_id | CSA3 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1get |
Chain | Residue | Details |
A | CYS44 | |
A | CYS49 |
site_id | CSA4 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 1get |
Chain | Residue | Details |
B | CYS44 | |
B | CYS49 |