6TG9
Cryo-EM Structure of NADH reduced form of NAD+-dependent Formate Dehydrogenase from Rhodobacter capsulatus
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003954 | molecular_function | NADH dehydrogenase activity |
| A | 0008863 | molecular_function | formate dehydrogenase (NAD+) activity |
| A | 0015942 | biological_process | formate metabolic process |
| A | 0016020 | cellular_component | membrane |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0022904 | biological_process | respiratory electron transport chain |
| A | 0043546 | molecular_function | molybdopterin cofactor binding |
| A | 0045333 | biological_process | cellular respiration |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0051536 | molecular_function | iron-sulfur cluster binding |
| A | 0051537 | molecular_function | 2 iron, 2 sulfur cluster binding |
| A | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
| A | 1990204 | cellular_component | oxidoreductase complex |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0008137 | molecular_function | NADH dehydrogenase (ubiquinone) activity |
| B | 0010181 | molecular_function | FMN binding |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0051536 | molecular_function | iron-sulfur cluster binding |
| B | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
| B | 1902600 | biological_process | proton transmembrane transport |
| C | 0016491 | molecular_function | oxidoreductase activity |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0051536 | molecular_function | iron-sulfur cluster binding |
| C | 0051537 | molecular_function | 2 iron, 2 sulfur cluster binding |
| D | 0016491 | molecular_function | oxidoreductase activity |
| E | 0003954 | molecular_function | NADH dehydrogenase activity |
| E | 0008863 | molecular_function | formate dehydrogenase (NAD+) activity |
| E | 0015942 | biological_process | formate metabolic process |
| E | 0016020 | cellular_component | membrane |
| E | 0016491 | molecular_function | oxidoreductase activity |
| E | 0022904 | biological_process | respiratory electron transport chain |
| E | 0043546 | molecular_function | molybdopterin cofactor binding |
| E | 0045333 | biological_process | cellular respiration |
| E | 0046872 | molecular_function | metal ion binding |
| E | 0051536 | molecular_function | iron-sulfur cluster binding |
| E | 0051537 | molecular_function | 2 iron, 2 sulfur cluster binding |
| E | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
| E | 1990204 | cellular_component | oxidoreductase complex |
| F | 0000166 | molecular_function | nucleotide binding |
| F | 0008137 | molecular_function | NADH dehydrogenase (ubiquinone) activity |
| F | 0010181 | molecular_function | FMN binding |
| F | 0016491 | molecular_function | oxidoreductase activity |
| F | 0046872 | molecular_function | metal ion binding |
| F | 0051536 | molecular_function | iron-sulfur cluster binding |
| F | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
| F | 1902600 | biological_process | proton transmembrane transport |
| G | 0016491 | molecular_function | oxidoreductase activity |
| G | 0046872 | molecular_function | metal ion binding |
| G | 0051536 | molecular_function | iron-sulfur cluster binding |
| G | 0051537 | molecular_function | 2 iron, 2 sulfur cluster binding |
| H | 0016491 | molecular_function | oxidoreductase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 27 |
| Details | binding site for residue MGD A 1001 |
| Chain | Residue |
| A | ARG357 |
| A | HIS681 |
| A | ASN686 |
| A | SER699 |
| A | LYS704 |
| A | ASP730 |
| A | THR827 |
| A | ARG829 |
| A | TYR834 |
| A | ASN835 |
| A | VAL836 |
| A | CYS358 |
| A | ALA838 |
| A | GLN839 |
| A | ASN908 |
| A | TYR924 |
| A | LYS925 |
| A | MGD1002 |
| A | 6MO1003 |
| A | H2S1009 |
| A | CYS386 |
| A | LEU551 |
| A | GLU555 |
| A | GLN589 |
| A | GLY655 |
| A | GLU656 |
| A | SER661 |
| site_id | AC2 |
| Number of Residues | 32 |
| Details | binding site for residue MGD A 1002 |
| Chain | Residue |
| A | CYS261 |
| A | LYS295 |
| A | CYS386 |
| A | ILE419 |
| A | GLY420 |
| A | ALA421 |
| A | ASN422 |
| A | ASP425 |
| A | GLY426 |
| A | HIS427 |
| A | VAL447 |
| A | PRO449 |
| A | ARG450 |
| A | PRO470 |
| A | GLY471 |
| A | ASN473 |
| A | LEU551 |
| A | GLY552 |
| A | HIS556 |
| A | GLY588 |
| A | GLN589 |
| A | THR826 |
| A | GLY828 |
| A | ARG829 |
| A | ILE830 |
| A | LEU831 |
| A | GLN833 |
| A | ASN835 |
| A | HIS901 |
| A | LYS925 |
| A | MGD1001 |
| A | 6MO1003 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | binding site for residue 6MO A 1003 |
| Chain | Residue |
| A | CYS386 |
| A | MGD1001 |
| A | MGD1002 |
| A | H2S1009 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue FES A 1004 |
| Chain | Residue |
| A | CYS57 |
| A | VAL65 |
| A | GLY66 |
| A | CYS68 |
| A | CYS71 |
| A | CYS85 |
| site_id | AC5 |
| Number of Residues | 7 |
| Details | binding site for residue SF4 A 1005 |
| Chain | Residue |
| A | HIS117 |
| A | CYS121 |
| A | CYS124 |
| A | ALA126 |
| A | CYS130 |
| A | THR236 |
| A | ALA237 |
| site_id | AC6 |
| Number of Residues | 8 |
| Details | binding site for residue SF4 A 1006 |
| Chain | Residue |
| A | CYS182 |
| A | ILE183 |
| A | CYS185 |
| A | MET186 |
| A | CYS188 |
| A | ILE212 |
| A | CYS234 |
| A | THR236 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | binding site for residue SF4 A 1007 |
| Chain | Residue |
| A | CYS192 |
| A | CYS224 |
| A | SER226 |
| A | CYS227 |
| A | GLY228 |
| A | CYS230 |
| site_id | AC8 |
| Number of Residues | 9 |
| Details | binding site for residue SF4 A 1008 |
| Chain | Residue |
| A | CYS258 |
| A | TYR260 |
| A | CYS261 |
| A | GLY264 |
| A | CYS265 |
| A | PHE267 |
| A | CYS293 |
| A | LYS295 |
| A | VAL429 |
| site_id | AC9 |
| Number of Residues | 3 |
| Details | binding site for residue H2S A 1009 |
| Chain | Residue |
| A | CYS386 |
| A | MGD1001 |
| A | 6MO1003 |
| site_id | AD1 |
| Number of Residues | 15 |
| Details | binding site for residue FMN B 601 |
| Chain | Residue |
| B | GLY146 |
| B | ARG147 |
| B | GLY148 |
| B | LYS157 |
| B | ASN174 |
| B | ASP176 |
| B | GLU177 |
| B | TYR254 |
| B | GLY257 |
| B | GLU258 |
| B | GLU259 |
| B | ASN293 |
| B | ASN294 |
| B | SER297 |
| B | NAI603 |
| site_id | AD2 |
| Number of Residues | 8 |
| Details | binding site for residue SF4 B 602 |
| Chain | Residue |
| B | SER426 |
| B | CYS427 |
| B | THR429 |
| B | CYS430 |
| B | CYS433 |
| B | LEU470 |
| B | CYS471 |
| B | GLY474 |
| site_id | AD3 |
| Number of Residues | 14 |
| Details | binding site for residue NAI B 603 |
| Chain | Residue |
| A | ARG79 |
| B | ALA150 |
| B | LYS157 |
| B | GLU258 |
| B | GLU259 |
| B | LEU279 |
| B | PRO280 |
| B | VAL292 |
| B | LYS466 |
| B | SER469 |
| B | LEU470 |
| B | ALA472 |
| B | GLY475 |
| B | FMN601 |
| site_id | AD4 |
| Number of Residues | 6 |
| Details | binding site for residue FES G 201 |
| Chain | Residue |
| G | CYS77 |
| G | ALA79 |
| G | CYS82 |
| G | CYS116 |
| G | LEU119 |
| G | CYS120 |
| site_id | AD5 |
| Number of Residues | 27 |
| Details | binding site for residue MGD E 1001 |
| Chain | Residue |
| E | ARG357 |
| E | CYS358 |
| E | CYS386 |
| E | LEU551 |
| E | GLU555 |
| E | GLN589 |
| E | GLY655 |
| E | GLU656 |
| E | SER661 |
| E | HIS681 |
| E | ASN686 |
| E | SER699 |
| E | LYS704 |
| E | ASP730 |
| E | THR827 |
| E | ARG829 |
| E | TYR834 |
| E | ASN835 |
| E | VAL836 |
| E | ALA838 |
| E | GLN839 |
| E | ASN908 |
| E | TYR924 |
| E | LYS925 |
| E | MGD1002 |
| E | 6MO1003 |
| E | H2S1009 |
| site_id | AD6 |
| Number of Residues | 32 |
| Details | binding site for residue MGD E 1002 |
| Chain | Residue |
| E | CYS261 |
| E | LYS295 |
| E | CYS386 |
| E | ILE419 |
| E | GLY420 |
| E | ALA421 |
| E | ASN422 |
| E | ASP425 |
| E | GLY426 |
| E | HIS427 |
| E | VAL447 |
| E | PRO449 |
| E | ARG450 |
| E | PRO470 |
| E | GLY471 |
| E | ASN473 |
| E | LEU551 |
| E | GLY552 |
| E | HIS556 |
| E | GLY588 |
| E | GLN589 |
| E | THR826 |
| E | GLY828 |
| E | ARG829 |
| E | ILE830 |
| E | LEU831 |
| E | GLN833 |
| E | ASN835 |
| E | HIS901 |
| E | LYS925 |
| E | MGD1001 |
| E | 6MO1003 |
| site_id | AD7 |
| Number of Residues | 4 |
| Details | binding site for residue 6MO E 1003 |
| Chain | Residue |
| E | CYS386 |
| E | MGD1001 |
| E | MGD1002 |
| E | H2S1009 |
| site_id | AD8 |
| Number of Residues | 6 |
| Details | binding site for residue FES E 1004 |
| Chain | Residue |
| E | CYS57 |
| E | VAL65 |
| E | GLY66 |
| E | CYS68 |
| E | CYS71 |
| E | CYS85 |
| site_id | AD9 |
| Number of Residues | 7 |
| Details | binding site for residue SF4 E 1005 |
| Chain | Residue |
| E | HIS117 |
| E | CYS121 |
| E | CYS124 |
| E | ALA126 |
| E | CYS130 |
| E | THR236 |
| E | ALA237 |
| site_id | AE1 |
| Number of Residues | 8 |
| Details | binding site for residue SF4 E 1006 |
| Chain | Residue |
| E | CYS182 |
| E | ILE183 |
| E | CYS185 |
| E | MET186 |
| E | CYS188 |
| E | ILE212 |
| E | CYS234 |
| E | THR236 |
| site_id | AE2 |
| Number of Residues | 6 |
| Details | binding site for residue SF4 E 1007 |
| Chain | Residue |
| E | CYS192 |
| E | CYS224 |
| E | SER226 |
| E | CYS227 |
| E | GLY228 |
| E | CYS230 |
| site_id | AE3 |
| Number of Residues | 9 |
| Details | binding site for residue SF4 E 1008 |
| Chain | Residue |
| E | CYS258 |
| E | TYR260 |
| E | CYS261 |
| E | GLY264 |
| E | CYS265 |
| E | PHE267 |
| E | CYS293 |
| E | LYS295 |
| E | VAL429 |
| site_id | AE4 |
| Number of Residues | 3 |
| Details | binding site for residue H2S E 1009 |
| Chain | Residue |
| E | CYS386 |
| E | MGD1001 |
| E | 6MO1003 |
| site_id | AE5 |
| Number of Residues | 15 |
| Details | binding site for residue FMN F 601 |
| Chain | Residue |
| F | GLY146 |
| F | ARG147 |
| F | GLY148 |
| F | LYS157 |
| F | ASN174 |
| F | ASP176 |
| F | GLU177 |
| F | TYR254 |
| F | GLY257 |
| F | GLU258 |
| F | GLU259 |
| F | ASN293 |
| F | ASN294 |
| F | SER297 |
| F | NAI603 |
| site_id | AE6 |
| Number of Residues | 8 |
| Details | binding site for residue SF4 F 602 |
| Chain | Residue |
| F | SER426 |
| F | CYS427 |
| F | THR429 |
| F | CYS430 |
| F | CYS433 |
| F | LEU470 |
| F | CYS471 |
| F | GLY474 |
| site_id | AE7 |
| Number of Residues | 14 |
| Details | binding site for residue NAI F 603 |
| Chain | Residue |
| E | ARG79 |
| F | ALA150 |
| F | LYS157 |
| F | GLU258 |
| F | GLU259 |
| F | LEU279 |
| F | PRO280 |
| F | VAL292 |
| F | LYS466 |
| F | SER469 |
| F | LEU470 |
| F | ALA472 |
| F | GLY475 |
| F | FMN601 |
| site_id | AE8 |
| Number of Residues | 6 |
| Details | binding site for residue FES C 201 |
| Chain | Residue |
| C | CYS77 |
| C | ALA79 |
| C | CYS82 |
| C | CYS116 |
| C | LEU119 |
| C | CYS120 |
Functional Information from PROSITE/UniProt
| site_id | PS00198 |
| Number of Residues | 12 |
| Details | 4FE4S_FER_1 4Fe-4S ferredoxin-type iron-sulfur binding region signature. CiVCMrCVrACE |
| Chain | Residue | Details |
| A | CYS182-GLU193 | |
| A | CYS224-PRO235 |
| site_id | PS00551 |
| Number of Residues | 19 |
| Details | MOLYBDOPTERIN_PROK_1 Prokaryotic molybdopterin oxidoreductases signature 1. TtCay.CGVgCsFeAhmlgD |
| Chain | Residue | Details |
| A | THR256-ASP274 |
| site_id | PS00644 |
| Number of Residues | 16 |
| Details | COMPLEX1_51K_1 Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. GAGAYVCGEETSLLNS |
| Chain | Residue | Details |
| B | GLY250-SER265 |
| site_id | PS00645 |
| Number of Residues | 12 |
| Details | COMPLEX1_51K_2 Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. ESCGtCtPCRiG |
| Chain | Residue | Details |
| B | GLU425-GLY436 |
| site_id | PS00932 |
| Number of Residues | 28 |
| Details | MOLYBDOPTERIN_PROK_3 Prokaryotic molybdopterin oxidoreductases signature 3. AetrGIrDgDwVrLaSraGettlrAtVT |
| Chain | Residue | Details |
| A | ALA861-THR888 |
| site_id | PS01039 |
| Number of Residues | 14 |
| Details | SBP_BACTERIAL_3 Bacterial extracellular solute-binding proteins, family 3 signature. GFEMEVRVgAGAYV |
| Chain | Residue | Details |
| B | GLY242-VAL255 |
