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 | 0008863 | molecular_function | formate dehydrogenase (NAD+) activity |
A | 0015942 | biological_process | formate metabolic process |
A | 0016491 | molecular_function | oxidoreductase activity |
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 | 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 | 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 | 0051537 | molecular_function | 2 iron, 2 sulfur cluster binding |
D | 0016491 | molecular_function | oxidoreductase activity |
E | 0008863 | molecular_function | formate dehydrogenase (NAD+) activity |
E | 0015942 | biological_process | formate metabolic process |
E | 0016491 | molecular_function | oxidoreductase activity |
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 | 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 | 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 | 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 |