1MC5
Ternary complex of Human glutathione-dependent formaldehyde dehydrogenase with S-(hydroxymethyl)glutathione and NADH
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0001523 | biological_process | retinoid metabolic process |
| A | 0003016 | biological_process | respiratory system process |
| A | 0004022 | molecular_function | alcohol dehydrogenase (NAD+) activity |
| A | 0004024 | molecular_function | alcohol dehydrogenase (NAD+) activity, zinc-dependent |
| A | 0005504 | molecular_function | fatty acid binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0005829 | cellular_component | cytosol |
| A | 0006629 | biological_process | lipid metabolic process |
| A | 0008270 | molecular_function | zinc ion binding |
| A | 0009055 | molecular_function | electron transfer activity |
| A | 0010430 | biological_process | fatty acid omega-oxidation |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0018467 | molecular_function | formaldehyde dehydrogenase (NAD+) activity |
| A | 0032496 | biological_process | response to lipopolysaccharide |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0044281 | biological_process | small molecule metabolic process |
| A | 0045777 | biological_process | positive regulation of blood pressure |
| A | 0046294 | biological_process | formaldehyde catabolic process |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0051409 | biological_process | response to nitrosative stress |
| A | 0051775 | biological_process | response to redox state |
| A | 0051903 | molecular_function | S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity |
| A | 0070062 | cellular_component | extracellular exosome |
| A | 0106321 | molecular_function | S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity |
| A | 0106322 | molecular_function | S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity |
| B | 0001523 | biological_process | retinoid metabolic process |
| B | 0003016 | biological_process | respiratory system process |
| B | 0004022 | molecular_function | alcohol dehydrogenase (NAD+) activity |
| B | 0004024 | molecular_function | alcohol dehydrogenase (NAD+) activity, zinc-dependent |
| B | 0005504 | molecular_function | fatty acid binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0005829 | cellular_component | cytosol |
| B | 0006629 | biological_process | lipid metabolic process |
| B | 0008270 | molecular_function | zinc ion binding |
| B | 0009055 | molecular_function | electron transfer activity |
| B | 0010430 | biological_process | fatty acid omega-oxidation |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0018467 | molecular_function | formaldehyde dehydrogenase (NAD+) activity |
| B | 0032496 | biological_process | response to lipopolysaccharide |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0044281 | biological_process | small molecule metabolic process |
| B | 0045777 | biological_process | positive regulation of blood pressure |
| B | 0046294 | biological_process | formaldehyde catabolic process |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0051409 | biological_process | response to nitrosative stress |
| B | 0051775 | biological_process | response to redox state |
| B | 0051903 | molecular_function | S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity |
| B | 0070062 | cellular_component | extracellular exosome |
| B | 0106321 | molecular_function | S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity |
| B | 0106322 | molecular_function | S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 375 |
| Chain | Residue |
| A | CYS96 |
| A | CYS99 |
| A | CYS102 |
| A | CYS110 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ZN A 376 |
| Chain | Residue |
| A | NAD500 |
| A | CYS44 |
| A | THR46 |
| A | HIS66 |
| A | CYS173 |
| A | AHE404 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN B 375 |
| Chain | Residue |
| B | CYS96 |
| B | CYS99 |
| B | CYS102 |
| B | CYS110 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN B 376 |
| Chain | Residue |
| B | CYS44 |
| B | HIS66 |
| B | GLU67 |
| B | CYS173 |
| B | HOH667 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K A 400 |
| Chain | Residue |
| A | ALA186 |
| A | LYS187 |
| A | GLU189 |
| A | TYR263 |
| A | HOH608 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PO4 A 401 |
| Chain | Residue |
| A | LYS314 |
| A | HOH538 |
| A | HOH608 |
| A | HOH623 |
| B | LYS314 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PO4 B 402 |
| Chain | Residue |
| A | LYS83 |
| A | PO4403 |
| B | LYS83 |
| B | ASP86 |
| B | LYS158 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PO4 A 403 |
| Chain | Residue |
| A | LYS83 |
| A | ASP86 |
| A | LYS158 |
| B | LYS83 |
| B | PO4402 |
| site_id | AC9 |
| Number of Residues | 25 |
| Details | BINDING SITE FOR RESIDUE NAD A 500 |
| Chain | Residue |
| A | HIS45 |
| A | THR46 |
| A | TYR92 |
| A | CYS173 |
| A | THR177 |
| A | GLY198 |
| A | GLY200 |
| A | GLY201 |
| A | VAL202 |
| A | ASP222 |
| A | ILE223 |
| A | LYS227 |
| A | CYS267 |
| A | ILE268 |
| A | VAL291 |
| A | GLY292 |
| A | VAL293 |
| A | THR316 |
| A | ALA317 |
| A | PHE318 |
| A | ARG368 |
| A | ZN376 |
| A | AHE404 |
| A | HOH571 |
| A | HOH572 |
| site_id | BC1 |
| Number of Residues | 28 |
| Details | BINDING SITE FOR RESIDUE NAD B 501 |
| Chain | Residue |
| B | HIS45 |
| B | CYS173 |
| B | THR177 |
| B | GLY198 |
| B | LEU199 |
| B | GLY200 |
| B | GLY201 |
| B | VAL202 |
| B | ASP222 |
| B | ILE223 |
| B | LYS227 |
| B | CYS267 |
| B | ILE268 |
| B | VAL273 |
| B | VAL291 |
| B | GLY292 |
| B | VAL293 |
| B | THR316 |
| B | PHE318 |
| B | ARG368 |
| B | HOH516 |
| B | HOH548 |
| B | HOH565 |
| B | HOH616 |
| B | HOH622 |
| B | HOH675 |
| B | HOH691 |
| B | HOH699 |
| site_id | BC2 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE AHE A 404 |
| Chain | Residue |
| A | CYS173 |
| A | VAL293 |
| A | ZN376 |
| A | NAD500 |
| A | HOH529 |
| A | HOH606 |
| A | HOH611 |
| A | HOH644 |
| A | THR46 |
| A | ASP55 |
| A | PRO56 |
| A | GLU57 |
| A | HIS66 |
| A | TYR92 |
| A | ARG114 |
Functional Information from PROSITE/UniProt
| site_id | PS00059 |
| Number of Residues | 15 |
| Details | ADH_ZINC Zinc-containing alcohol dehydrogenases signature. GHEgAGIvesvGegV |
| Chain | Residue | Details |
| A | GLY65-VAL79 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 14 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:3365377 |
| Chain | Residue | Details |
| A | HIS45 | |
| B | GLY97 | |
| B | LYS100 | |
| B | LEU103 | |
| B | GLN111 | |
| B | GLY174 | |
| A | GLU67 | |
| A | GLY97 | |
| A | LYS100 | |
| A | LEU103 | |
| A | GLN111 | |
| A | GLY174 | |
| B | HIS45 | |
| B | GLU67 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | SITE: Important for FDH activity and activation by fatty acids => ECO:0000269|PubMed:8460164, ECO:0000269|PubMed:8494891 |
| Chain | Residue | Details |
| A | VAL115 | |
| B | VAL115 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | MOD_RES: N-acetylalanine => ECO:0007744|PubMed:19413330 |
| Chain | Residue | Details |
| A | ASN2 | |
| B | ASN2 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P28474 |
| Chain | Residue | Details |
| A | GLU233 | |
| A | GLY315 | |
| B | GLU233 | |
| B | GLY315 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | LYS247 | |
| B | LYS247 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | VAL324 | |
| A | PHE351 | |
| B | VAL324 | |
| B | PHE351 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1teh |
| Chain | Residue | Details |
| A | THR46 | |
| A | HIS45 |
| site_id | CSA2 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1teh |
| Chain | Residue | Details |
| B | THR46 | |
| B | HIS45 |
| site_id | CSA3 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1teh |
| Chain | Residue | Details |
| A | ASP55 |
| site_id | CSA4 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1teh |
| Chain | Residue | Details |
| B | ASP55 |
| site_id | MCSA1 |
| Number of Residues | 12 |
| Details | M-CSA 464 |
| Chain | Residue | Details |
| A | HIS45 | metal ligand |
| A | VAL115 | activator |
| A | GLY174 | metal ligand |
| A | THR369 | steric role |
| A | THR46 | proton shuttle (general acid/base) |
| A | ASP47 | proton shuttle (general acid/base) |
| A | GLU67 | metal ligand |
| A | GLY68 | metal ligand |
| A | GLY97 | metal ligand |
| A | LYS100 | metal ligand |
| A | LEU103 | metal ligand |
| A | GLN111 | metal ligand |
| site_id | MCSA2 |
| Number of Residues | 12 |
| Details | M-CSA 464 |
| Chain | Residue | Details |
| B | HIS45 | metal ligand |
| B | VAL115 | activator |
| B | GLY174 | metal ligand |
| B | THR369 | steric role |
| B | THR46 | proton shuttle (general acid/base) |
| B | ASP47 | proton shuttle (general acid/base) |
| B | GLU67 | metal ligand |
| B | GLY68 | metal ligand |
| B | GLY97 | metal ligand |
| B | LYS100 | metal ligand |
| B | LEU103 | metal ligand |
| B | GLN111 | metal ligand |
