6HG8
Crystal structure of the R460G disease-causing mutant of the human dihydrolipoamide dehydrogenase.
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0001669 | cellular_component | acrosomal vesicle |
| A | 0004148 | molecular_function | dihydrolipoyl dehydrogenase (NADH) activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0005759 | cellular_component | mitochondrial matrix |
| A | 0005929 | cellular_component | cilium |
| 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 | 0009083 | biological_process | branched-chain amino acid 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 | 0019474 | biological_process | L-lysine catabolic process to acetyl-CoA |
| A | 0031410 | cellular_component | cytoplasmic vesicle |
| A | 0031514 | cellular_component | motile cilium |
| A | 0043159 | cellular_component | acrosomal matrix |
| A | 0045252 | cellular_component | oxoglutarate dehydrogenase complex |
| A | 0045254 | cellular_component | pyruvate dehydrogenase complex |
| A | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| A | 0120551 | biological_process | 2-oxoglutarate decarboxylation to succinyl-CoA |
| A | 0120552 | biological_process | branched-chain alpha-keto acid decarboxylation to branched-chain acyl-CoA |
| A | 0160157 | cellular_component | branched-chain alpha-ketoacid dehydrogenase complex |
| A | 0160167 | cellular_component | oxoadipate dehydrogenase complex |
| B | 0001669 | cellular_component | acrosomal vesicle |
| B | 0004148 | molecular_function | dihydrolipoyl dehydrogenase (NADH) activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0005759 | cellular_component | mitochondrial matrix |
| B | 0005929 | cellular_component | cilium |
| 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 | 0009083 | biological_process | branched-chain amino acid 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 | 0019474 | biological_process | L-lysine catabolic process to acetyl-CoA |
| B | 0031410 | cellular_component | cytoplasmic vesicle |
| B | 0031514 | cellular_component | motile cilium |
| B | 0043159 | cellular_component | acrosomal matrix |
| B | 0045252 | cellular_component | oxoglutarate dehydrogenase complex |
| B | 0045254 | cellular_component | pyruvate dehydrogenase complex |
| B | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| B | 0120551 | biological_process | 2-oxoglutarate decarboxylation to succinyl-CoA |
| B | 0120552 | biological_process | branched-chain alpha-keto acid decarboxylation to branched-chain acyl-CoA |
| B | 0160157 | cellular_component | branched-chain alpha-ketoacid dehydrogenase complex |
| B | 0160167 | cellular_component | oxoadipate dehydrogenase complex |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 37 |
| Details | binding site for residue FAD A 501 |
| Chain | Residue |
| A | ILE12 |
| A | THR44 |
| A | CYS45 |
| A | VAL48 |
| A | GLY49 |
| A | CYS50 |
| A | LYS54 |
| A | GLY117 |
| A | TYR118 |
| A | GLY119 |
| A | ALA147 |
| A | GLY13 |
| A | THR148 |
| A | GLY149 |
| A | SER150 |
| A | SER168 |
| A | ARG280 |
| A | PHE283 |
| A | GLY319 |
| A | ASP320 |
| A | MET326 |
| A | LEU327 |
| A | GLY15 |
| A | ALA328 |
| A | HIS329 |
| A | TYR359 |
| A | HOH702 |
| A | HOH714 |
| A | HOH749 |
| A | HOH896 |
| B | HIS452 |
| A | PRO16 |
| A | GLY17 |
| A | GLU36 |
| A | LYS37 |
| A | ASN38 |
| A | GLY43 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 A 502 |
| Chain | Residue |
| A | LEU210 |
| A | GLY211 |
| A | HIS212 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 A 503 |
| Chain | Residue |
| A | ARG299 |
| A | ARG301 |
| A | GLY324 |
| A | HOH891 |
| site_id | AC4 |
| Number of Residues | 10 |
| Details | binding site for residue SO4 A 504 |
| Chain | Residue |
| A | THR284 |
| A | ASN286 |
| A | LEU287 |
| A | GLY288 |
| A | LEU289 |
| A | GLU290 |
| A | GLU291 |
| A | HOH606 |
| A | HOH659 |
| A | HOH897 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 A 505 |
| Chain | Residue |
| A | LYS124 |
| A | PRO313 |
| A | ASN314 |
| A | HOH748 |
| A | HOH813 |
| B | ARG414 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 A 506 |
| Chain | Residue |
| A | HIS64 |
| A | GLY68 |
| A | LYS69 |
| A | HOH670 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | binding site for residue TRS A 507 |
| Chain | Residue |
| A | LYS249 |
| A | SER250 |
| A | ASP251 |
| B | GLN126 |
| site_id | AC8 |
| Number of Residues | 40 |
| Details | binding site for residue FAD B 501 |
| Chain | Residue |
| B | LEU327 |
| B | ALA328 |
| B | HIS329 |
| B | TYR359 |
| B | HOH650 |
| B | HOH651 |
| B | HOH711 |
| B | HOH819 |
| B | HOH884 |
| A | HIS452 |
| B | ILE12 |
| B | GLY13 |
| B | GLY15 |
| B | PRO16 |
| B | GLY17 |
| B | GLU36 |
| B | LYS37 |
| B | ASN38 |
| B | GLY43 |
| B | THR44 |
| B | CYS45 |
| B | VAL48 |
| B | GLY49 |
| B | CYS50 |
| B | SER53 |
| B | LYS54 |
| B | GLY117 |
| B | TYR118 |
| B | GLY119 |
| B | ALA147 |
| B | THR148 |
| B | GLY149 |
| B | SER150 |
| B | SER168 |
| B | ILE189 |
| B | ARG280 |
| B | PHE283 |
| B | GLY319 |
| B | ASP320 |
| B | MET326 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 B 502 |
| Chain | Residue |
| B | GLY187 |
| B | GLY215 |
| B | HOH707 |
| B | HOH768 |
| B | HOH784 |
| B | HOH911 |
| site_id | AD1 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 B 503 |
| Chain | Residue |
| A | HOH640 |
| B | ARG393 |
| B | ASN397 |
| B | LEU455 |
| B | HOH607 |
| site_id | AD2 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 B 504 |
| Chain | Residue |
| B | LEU210 |
| B | GLY211 |
| B | HIS212 |
| site_id | AD3 |
| Number of Residues | 9 |
| Details | binding site for residue SO4 B 505 |
| Chain | Residue |
| B | THR284 |
| B | ASN286 |
| B | LEU287 |
| B | GLY288 |
| B | LEU289 |
| B | GLU290 |
| B | HOH609 |
| B | HOH703 |
| B | HOH830 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 B 506 |
| Chain | Residue |
| B | HIS64 |
| B | GLY68 |
| B | LYS69 |
| B | HOH610 |
| site_id | AD5 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 B 507 |
| Chain | Residue |
| B | ARG299 |
| B | ARG301 |
| B | GLY324 |
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 | GLY42-PRO52 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton acceptor","evidences":[{"source":"UniProtKB","id":"P09624","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 54 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"15946682","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | Site: {"description":"Important for interaction with PDHX and activity of multienzyme pyruvate dehydrogenase complex","evidences":[{"source":"PubMed","id":"20385101","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 14 |
| Details | Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"O08749","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 10 |
| Details | Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"O08749","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"O08749","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q6P6R2","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"O08749","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
