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 (NADH) activity |
| A | 0004375 | molecular_function | glycine dehydrogenase (decarboxylating) activity |
| A | 0004591 | molecular_function | oxoglutarate dehydrogenase (succinyl-transferring) 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 | pyruvate decarboxylation to acetyl-CoA |
| 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 | L-isoleucine catabolic process |
| A | 0006552 | biological_process | L-leucine catabolic process |
| A | 0006564 | biological_process | L-serine biosynthetic process |
| A | 0006574 | biological_process | L-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 | 0045333 | biological_process | cellular respiration |
| A | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| B | 0004148 | molecular_function | dihydrolipoyl dehydrogenase (NADH) activity |
| B | 0004375 | molecular_function | glycine dehydrogenase (decarboxylating) activity |
| B | 0004591 | molecular_function | oxoglutarate dehydrogenase (succinyl-transferring) 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 | pyruvate decarboxylation to acetyl-CoA |
| 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 | L-isoleucine catabolic process |
| B | 0006552 | biological_process | L-leucine catabolic process |
| B | 0006564 | biological_process | L-serine biosynthetic process |
| B | 0006574 | biological_process | L-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 | 0045333 | biological_process | cellular respiration |
| 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 | Active site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"9538259","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 30 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"9538259","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"FEB-2005","submissionDatabase":"PDB data bank","title":"Crystal structure of yeast lipoamide dehydrogenase complexed with NAD+.","authors":["Adachi W.","Suzuki K.","Tsunoda M.","Sekiguchi T.","Reed L.J.","Takenaka A."]}}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 24 |
| Details | Binding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
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 |
