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 activity |
A | 0005515 | molecular_function | protein binding |
A | 0005634 | cellular_component | nucleus |
A | 0005739 | cellular_component | mitochondrion |
A | 0005759 | cellular_component | mitochondrial matrix |
A | 0005929 | cellular_component | cilium |
A | 0006086 | biological_process | acetyl-CoA biosynthetic process from pyruvate |
A | 0006120 | biological_process | mitochondrial electron transport, NADH to ubiquinone |
A | 0006508 | biological_process | proteolysis |
A | 0007369 | biological_process | gastrulation |
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 | 0031410 | cellular_component | cytoplasmic vesicle |
A | 0031514 | cellular_component | motile cilium |
A | 0034604 | molecular_function | pyruvate dehydrogenase (NAD+) activity |
A | 0042391 | biological_process | regulation of membrane potential |
A | 0043159 | cellular_component | acrosomal matrix |
A | 0045252 | cellular_component | oxoglutarate dehydrogenase complex |
A | 0045254 | cellular_component | pyruvate dehydrogenase complex |
A | 0047101 | molecular_function | branched-chain alpha-keto acid dehydrogenase activity |
A | 0048240 | biological_process | sperm capacitation |
A | 0050660 | molecular_function | flavin adenine dinucleotide binding |
A | 0160157 | cellular_component | branched-chain alpha-ketoacid dehydrogenase complex |
A | 0160167 | cellular_component | oxoadipate dehydrogenase complex |
A | 1902493 | cellular_component | acetyltransferase complex |
B | 0001669 | cellular_component | acrosomal vesicle |
B | 0004148 | molecular_function | dihydrolipoyl dehydrogenase activity |
B | 0005515 | molecular_function | protein binding |
B | 0005634 | cellular_component | nucleus |
B | 0005739 | cellular_component | mitochondrion |
B | 0005759 | cellular_component | mitochondrial matrix |
B | 0005929 | cellular_component | cilium |
B | 0006086 | biological_process | acetyl-CoA biosynthetic process from pyruvate |
B | 0006120 | biological_process | mitochondrial electron transport, NADH to ubiquinone |
B | 0006508 | biological_process | proteolysis |
B | 0007369 | biological_process | gastrulation |
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 | 0031410 | cellular_component | cytoplasmic vesicle |
B | 0031514 | cellular_component | motile cilium |
B | 0034604 | molecular_function | pyruvate dehydrogenase (NAD+) activity |
B | 0042391 | biological_process | regulation of membrane potential |
B | 0043159 | cellular_component | acrosomal matrix |
B | 0045252 | cellular_component | oxoglutarate dehydrogenase complex |
B | 0045254 | cellular_component | pyruvate dehydrogenase complex |
B | 0047101 | molecular_function | branched-chain alpha-keto acid dehydrogenase activity |
B | 0048240 | biological_process | sperm capacitation |
B | 0050660 | molecular_function | flavin adenine dinucleotide binding |
B | 0160157 | cellular_component | branched-chain alpha-ketoacid dehydrogenase complex |
B | 0160167 | cellular_component | oxoadipate dehydrogenase complex |
B | 1902493 | cellular_component | acetyltransferase 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 | ACT_SITE: Proton acceptor => ECO:0000250|UniProtKB:P09624 |
Chain | Residue | Details |
A | HIS452 | |
B | HIS452 |
site_id | SWS_FT_FI2 |
Number of Residues | 20 |
Details | BINDING: BINDING => ECO:0000269|PubMed:15946682 |
Chain | Residue | Details |
A | GLU36 | |
A | MET326 | |
B | GLU36 | |
B | LYS54 | |
B | GLY119 | |
B | THR148 | |
B | GLY185 | |
B | GLU208 | |
B | VAL243 | |
B | GLY279 | |
B | ASP320 | |
A | LYS54 | |
B | MET326 | |
A | GLY119 | |
A | THR148 | |
A | GLY185 | |
A | GLU208 | |
A | VAL243 | |
A | GLY279 | |
A | ASP320 |
site_id | SWS_FT_FI3 |
Number of Residues | 4 |
Details | SITE: Important for interaction with PDHX and activity of multienzyme pyruvate dehydrogenase complex => ECO:0000269|PubMed:20385101 |
Chain | Residue | Details |
A | ASP413 | |
A | TYR438 | |
B | ASP413 | |
B | TYR438 |
site_id | SWS_FT_FI4 |
Number of Residues | 14 |
Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:O08749 |
Chain | Residue | Details |
A | LYS31 | |
B | LYS87 | |
B | LYS97 | |
B | LYS108 | |
B | LYS375 | |
B | LYS470 | |
A | LYS69 | |
A | LYS87 | |
A | LYS97 | |
A | LYS108 | |
A | LYS375 | |
A | LYS470 | |
B | LYS31 | |
B | LYS69 |
site_id | SWS_FT_FI5 |
Number of Residues | 10 |
Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:O08749 |
Chain | Residue | Details |
A | LYS124 | |
B | LYS395 | |
A | LYS131 | |
A | LYS238 | |
A | LYS242 | |
A | LYS395 | |
B | LYS124 | |
B | LYS131 | |
B | LYS238 | |
B | LYS242 |
site_id | SWS_FT_FI6 |
Number of Residues | 2 |
Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:O08749 |
Chain | Residue | Details |
A | SER250 | |
B | SER250 |
site_id | SWS_FT_FI7 |
Number of Residues | 2 |
Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q6P6R2 |
Chain | Residue | Details |
A | SER262 | |
B | SER262 |
site_id | SWS_FT_FI8 |
Number of Residues | 4 |
Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:O08749 |
Chain | Residue | Details |
A | LYS311 | |
A | LYS385 | |
B | LYS311 | |
B | LYS385 |
site_id | SWS_FT_FI9 |
Number of Residues | 2 |
Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
Chain | Residue | Details |
A | LYS382 | |
B | LYS382 |
site_id | SWS_FT_FI10 |
Number of Residues | 2 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
A | SER467 | |
B | SER467 |