3IAM
Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, reduced, 2 mol/ASU, with bound NADH
Functional Information from GO Data
Chain | GOid | namespace | contents |
1 | 0005886 | cellular_component | plasma membrane |
1 | 0008137 | molecular_function | NADH dehydrogenase (ubiquinone) activity |
1 | 0010181 | molecular_function | FMN binding |
1 | 0045271 | cellular_component | respiratory chain complex I |
1 | 0046872 | molecular_function | metal ion binding |
1 | 0048038 | molecular_function | quinone binding |
1 | 0051287 | molecular_function | NAD binding |
1 | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
1 | 1902600 | biological_process | proton transmembrane transport |
2 | 0003954 | molecular_function | NADH dehydrogenase activity |
2 | 0005886 | cellular_component | plasma membrane |
2 | 0016491 | molecular_function | oxidoreductase activity |
2 | 0045271 | cellular_component | respiratory chain complex I |
2 | 0046872 | molecular_function | metal ion binding |
2 | 0048038 | molecular_function | quinone binding |
2 | 0051537 | molecular_function | 2 iron, 2 sulfur cluster binding |
3 | 0003954 | molecular_function | NADH dehydrogenase activity |
3 | 0005886 | cellular_component | plasma membrane |
3 | 0008137 | molecular_function | NADH dehydrogenase (ubiquinone) activity |
3 | 0016020 | cellular_component | membrane |
3 | 0016491 | molecular_function | oxidoreductase activity |
3 | 0016651 | molecular_function | oxidoreductase activity, acting on NAD(P)H |
3 | 0042773 | biological_process | ATP synthesis coupled electron transport |
3 | 0043546 | molecular_function | molybdopterin cofactor binding |
3 | 0045333 | biological_process | cellular respiration |
3 | 0046872 | molecular_function | metal ion binding |
3 | 0048038 | molecular_function | quinone binding |
3 | 0051536 | molecular_function | iron-sulfur cluster binding |
3 | 0051537 | molecular_function | 2 iron, 2 sulfur cluster binding |
3 | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
3 | 1902600 | biological_process | proton transmembrane transport |
4 | 0005886 | cellular_component | plasma membrane |
4 | 0016651 | molecular_function | oxidoreductase activity, acting on NAD(P)H |
4 | 0048038 | molecular_function | quinone binding |
4 | 0050136 | molecular_function | NADH:ubiquinone reductase (non-electrogenic) activity |
4 | 0051287 | molecular_function | NAD binding |
5 | 0005886 | cellular_component | plasma membrane |
5 | 0008137 | molecular_function | NADH dehydrogenase (ubiquinone) activity |
5 | 0016651 | molecular_function | oxidoreductase activity, acting on NAD(P)H |
5 | 0048038 | molecular_function | quinone binding |
5 | 0050136 | molecular_function | NADH:ubiquinone reductase (non-electrogenic) activity |
5 | 1902600 | biological_process | proton transmembrane transport |
6 | 0005506 | molecular_function | iron ion binding |
6 | 0005886 | cellular_component | plasma membrane |
6 | 0008137 | molecular_function | NADH dehydrogenase (ubiquinone) activity |
6 | 0009060 | biological_process | aerobic respiration |
6 | 0015990 | biological_process | electron transport coupled proton transport |
6 | 0046872 | molecular_function | metal ion binding |
6 | 0048038 | molecular_function | quinone binding |
6 | 0050136 | molecular_function | NADH:ubiquinone reductase (non-electrogenic) activity |
6 | 0051536 | molecular_function | iron-sulfur cluster binding |
6 | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
7 | 0005886 | cellular_component | plasma membrane |
7 | 0008199 | molecular_function | ferric iron binding |
7 | 0016226 | biological_process | iron-sulfur cluster assembly |
7 | 0048038 | molecular_function | quinone binding |
9 | 0003954 | molecular_function | NADH dehydrogenase activity |
9 | 0005506 | molecular_function | iron ion binding |
9 | 0005886 | cellular_component | plasma membrane |
9 | 0009060 | biological_process | aerobic respiration |
9 | 0016020 | cellular_component | membrane |
9 | 0016651 | molecular_function | oxidoreductase activity, acting on NAD(P)H |
9 | 0046872 | molecular_function | metal ion binding |
9 | 0048038 | molecular_function | quinone binding |
9 | 0050136 | molecular_function | NADH:ubiquinone reductase (non-electrogenic) activity |
9 | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
A | 0005886 | cellular_component | plasma membrane |
A | 0008137 | molecular_function | NADH dehydrogenase (ubiquinone) activity |
A | 0010181 | molecular_function | FMN binding |
A | 0045271 | cellular_component | respiratory chain complex I |
A | 0046872 | molecular_function | metal ion binding |
A | 0048038 | molecular_function | quinone binding |
A | 0051287 | molecular_function | NAD binding |
A | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
A | 1902600 | biological_process | proton transmembrane transport |
B | 0003954 | molecular_function | NADH dehydrogenase activity |
B | 0005886 | cellular_component | plasma membrane |
B | 0016491 | molecular_function | oxidoreductase activity |
B | 0045271 | cellular_component | respiratory chain complex I |
B | 0046872 | molecular_function | metal ion binding |
B | 0048038 | molecular_function | quinone binding |
B | 0051537 | molecular_function | 2 iron, 2 sulfur cluster binding |
C | 0003954 | molecular_function | NADH dehydrogenase activity |
C | 0005886 | cellular_component | plasma membrane |
C | 0008137 | molecular_function | NADH dehydrogenase (ubiquinone) activity |
C | 0016020 | cellular_component | membrane |
C | 0016491 | molecular_function | oxidoreductase activity |
C | 0016651 | molecular_function | oxidoreductase activity, acting on NAD(P)H |
C | 0042773 | biological_process | ATP synthesis coupled electron transport |
C | 0043546 | molecular_function | molybdopterin cofactor binding |
C | 0045333 | biological_process | cellular respiration |
C | 0046872 | molecular_function | metal ion binding |
C | 0048038 | molecular_function | quinone binding |
C | 0051536 | molecular_function | iron-sulfur cluster binding |
C | 0051537 | molecular_function | 2 iron, 2 sulfur cluster binding |
C | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
C | 1902600 | biological_process | proton transmembrane transport |
D | 0005886 | cellular_component | plasma membrane |
D | 0016651 | molecular_function | oxidoreductase activity, acting on NAD(P)H |
D | 0048038 | molecular_function | quinone binding |
D | 0050136 | molecular_function | NADH:ubiquinone reductase (non-electrogenic) activity |
D | 0051287 | molecular_function | NAD binding |
E | 0005886 | cellular_component | plasma membrane |
E | 0008137 | molecular_function | NADH dehydrogenase (ubiquinone) activity |
E | 0016651 | molecular_function | oxidoreductase activity, acting on NAD(P)H |
E | 0048038 | molecular_function | quinone binding |
E | 0050136 | molecular_function | NADH:ubiquinone reductase (non-electrogenic) activity |
E | 1902600 | biological_process | proton transmembrane transport |
F | 0005506 | molecular_function | iron ion binding |
F | 0005886 | cellular_component | plasma membrane |
F | 0008137 | molecular_function | NADH dehydrogenase (ubiquinone) activity |
F | 0009060 | biological_process | aerobic respiration |
F | 0015990 | biological_process | electron transport coupled proton transport |
F | 0046872 | molecular_function | metal ion binding |
F | 0048038 | molecular_function | quinone binding |
F | 0050136 | molecular_function | NADH:ubiquinone reductase (non-electrogenic) activity |
F | 0051536 | molecular_function | iron-sulfur cluster binding |
F | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
G | 0003954 | molecular_function | NADH dehydrogenase activity |
G | 0005506 | molecular_function | iron ion binding |
G | 0005886 | cellular_component | plasma membrane |
G | 0009060 | biological_process | aerobic respiration |
G | 0016020 | cellular_component | membrane |
G | 0016651 | molecular_function | oxidoreductase activity, acting on NAD(P)H |
G | 0046872 | molecular_function | metal ion binding |
G | 0048038 | molecular_function | quinone binding |
G | 0050136 | molecular_function | NADH:ubiquinone reductase (non-electrogenic) activity |
G | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
H | 0005886 | cellular_component | plasma membrane |
H | 0008199 | molecular_function | ferric iron binding |
H | 0016226 | biological_process | iron-sulfur cluster assembly |
H | 0048038 | molecular_function | quinone binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE SF4 6 182 |
Chain | Residue |
4 | ARG84 |
6 | PRO141 |
4 | HIS169 |
6 | CYS45 |
6 | CYS46 |
6 | GLY82 |
6 | ARG83 |
6 | ALA110 |
6 | CYS111 |
6 | CYS140 |
site_id | AC2 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE SF4 9 183 |
Chain | Residue |
9 | HIS41 |
9 | CYS63 |
9 | ILE68 |
9 | CYS98 |
9 | ILE99 |
9 | PHE100 |
9 | CYS101 |
9 | GLY102 |
9 | CYS104 |
site_id | AC3 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE SF4 9 184 |
Chain | Residue |
9 | CYS53 |
9 | ILE54 |
9 | CYS56 |
9 | SER57 |
9 | CYS59 |
9 | CYS108 |
9 | THR110 |
9 | ALA112 |
site_id | AC4 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE SF4 3 784 |
Chain | Residue |
3 | HIS115 |
3 | CYS119 |
3 | CYS122 |
3 | CYS128 |
3 | LEU130 |
3 | VAL232 |
3 | GLY233 |
site_id | AC5 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE SF4 3 785 |
Chain | Residue |
3 | CYS181 |
3 | ILE182 |
3 | CYS184 |
3 | ARG186 |
3 | CYS187 |
3 | CYS230 |
3 | VAL232 |
3 | ALA234 |
site_id | AC6 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE SF4 3 786 |
Chain | Residue |
3 | CYS256 |
3 | CYS259 |
3 | VAL261 |
3 | GLY262 |
3 | CYS263 |
3 | ILE290 |
3 | CYS291 |
3 | PRO407 |
3 | ILE408 |
site_id | AC7 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE FES 3 787 |
Chain | Residue |
3 | CYS34 |
3 | SER35 |
3 | GLY43 |
3 | ALA44 |
3 | CYS45 |
3 | ARG46 |
3 | CYS48 |
3 | CYS83 |
site_id | AC8 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE SF4 1 439 |
Chain | Residue |
1 | PRO199 |
1 | SER352 |
1 | CYS353 |
1 | LYS355 |
1 | CYS356 |
1 | CYS359 |
1 | SER398 |
1 | PHE399 |
1 | CYS400 |
site_id | AC9 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE FES 2 182 |
Chain | Residue |
2 | CYS83 |
2 | SER87 |
2 | CYS88 |
2 | CYS124 |
2 | LEU125 |
2 | GLY126 |
2 | SER127 |
2 | CYS128 |
site_id | BC1 |
Number of Residues | 16 |
Details | BINDING SITE FOR RESIDUE FMN 1 440 |
Chain | Residue |
1 | GLY64 |
1 | ARG65 |
1 | GLY66 |
1 | LYS75 |
1 | ASN92 |
1 | ASP94 |
1 | SER96 |
1 | GLY183 |
1 | GLU184 |
1 | GLU185 |
1 | ILE218 |
1 | ASN219 |
1 | ASN220 |
1 | THR223 |
1 | PRO401 |
1 | NAI441 |
site_id | BC2 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE NAI 1 441 |
Chain | Residue |
1 | TYR180 |
1 | GLU185 |
1 | LYS202 |
1 | PHE205 |
1 | THR325 |
1 | PRO401 |
1 | FMN440 |
1 | GLY66 |
1 | GLY67 |
1 | ALA68 |
1 | PHE70 |
1 | LYS75 |
1 | PHE78 |
1 | GLU97 |
site_id | BC3 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE MG 3 788 |
Chain | Residue |
3 | LEU274 |
3 | ASP302 |
site_id | BC4 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE MG 3 789 |
Chain | Residue |
3 | HIS167 |
7 | GLU32 |
site_id | BC5 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE MG 5 208 |
Chain | Residue |
5 | HIS144 |
site_id | BC6 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE MG 1 442 |
Chain | Residue |
1 | HIS35 |
D | GLU210 |
site_id | BC7 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE CA 7 204 |
Chain | Residue |
3 | ASP165 |
3 | HIS168 |
7 | GLU32 |
7 | GLU34 |
7 | SER60 |
7 | GLY64 |
site_id | BC8 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MG 4 410 |
Chain | Residue |
4 | VAL223 |
4 | ALA384 |
4 | LYS386 |
4 | GLU388 |
site_id | BC9 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE MG 2 206 |
Chain | Residue |
1 | HIS350 |
2 | SER68 |
2 | GLU123 |
site_id | CC1 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE SF4 F 182 |
Chain | Residue |
D | ARG84 |
D | HIS169 |
F | CYS45 |
F | CYS46 |
F | GLY82 |
F | ARG83 |
F | ALA110 |
F | CYS111 |
F | CYS140 |
F | PRO141 |
site_id | CC2 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE SF4 G 183 |
Chain | Residue |
G | HIS41 |
G | CYS63 |
G | ILE68 |
G | CYS98 |
G | ILE99 |
G | PHE100 |
G | CYS101 |
G | GLY102 |
G | CYS104 |
site_id | CC3 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE SF4 G 184 |
Chain | Residue |
G | CYS53 |
G | ILE54 |
G | CYS56 |
G | SER57 |
G | CYS59 |
G | CYS108 |
G | THR110 |
G | ALA112 |
site_id | CC4 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE SF4 C 784 |
Chain | Residue |
C | HIS115 |
C | CYS119 |
C | CYS122 |
C | CYS128 |
C | LEU130 |
C | VAL232 |
C | GLY233 |
site_id | CC5 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE SF4 C 785 |
Chain | Residue |
C | CYS181 |
C | ILE182 |
C | CYS184 |
C | CYS187 |
C | CYS230 |
C | VAL232 |
C | ALA234 |
C | LEU235 |
site_id | CC6 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE SF4 C 786 |
Chain | Residue |
C | CYS256 |
C | LEU258 |
C | CYS259 |
C | VAL261 |
C | GLY262 |
C | CYS263 |
C | CYS291 |
site_id | CC7 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE FES C 787 |
Chain | Residue |
C | CYS34 |
C | SER35 |
C | GLY43 |
C | ALA44 |
C | CYS45 |
C | ARG46 |
C | CYS48 |
C | CYS83 |
site_id | CC8 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE SF4 A 439 |
Chain | Residue |
A | PRO199 |
A | SER352 |
A | CYS353 |
A | LYS355 |
A | CYS356 |
A | CYS359 |
A | PHE399 |
A | CYS400 |
A | ALA403 |
site_id | CC9 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE FES B 182 |
Chain | Residue |
B | CYS83 |
B | THR85 |
B | SER87 |
B | CYS88 |
B | CYS124 |
B | LEU125 |
B | GLY126 |
B | SER127 |
B | CYS128 |
site_id | DC1 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE FMN A 440 |
Chain | Residue |
A | GLY64 |
A | GLY66 |
A | LYS75 |
A | ASN92 |
A | ASP94 |
A | SER96 |
A | GLY183 |
A | GLU184 |
A | GLU185 |
A | ILE218 |
A | ASN219 |
A | ASN220 |
A | THR223 |
A | PRO401 |
A | NAI441 |
site_id | DC2 |
Number of Residues | 13 |
Details | BINDING SITE FOR RESIDUE NAI A 441 |
Chain | Residue |
A | GLY66 |
A | GLY67 |
A | ALA68 |
A | PHE70 |
A | LYS75 |
A | SER96 |
A | GLU97 |
A | TYR180 |
A | GLU185 |
A | LYS202 |
A | PHE205 |
A | THR325 |
A | FMN440 |
site_id | DC3 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE MG C 788 |
Chain | Residue |
C | LEU274 |
C | ASP302 |
site_id | DC4 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE MG C 789 |
Chain | Residue |
C | HIS167 |
H | GLU32 |
site_id | DC5 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE MG E 208 |
Chain | Residue |
E | HIS144 |
site_id | DC6 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE MG A 442 |
Chain | Residue |
4 | GLU210 |
A | HIS35 |
site_id | DC7 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE CA H 204 |
Chain | Residue |
C | ASP165 |
C | HIS168 |
H | GLU32 |
H | GLU34 |
H | GLY64 |
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. CiGCSlCAaACP |
Chain | Residue | Details |
9 | CYS53-PRO64 | |
9 | CYS98-PRO109 |
site_id | PS00535 |
Number of Residues | 12 |
Details | COMPLEX1_49K Respiratory chain NADH dehydrogenase 49 Kd subunit signature. LHTGfEKTmEhR |
Chain | Residue | Details |
4 | LEU62-ARG73 |
site_id | PS00542 |
Number of Residues | 22 |
Details | COMPLEX1_30K Respiratory chain NADH dehydrogenase 30 Kd subunit signature. EREvyDLFgivfegHpdlRkIL |
Chain | Residue | Details |
5 | GLU115-LEU136 |
site_id | PS00641 |
Number of Residues | 18 |
Details | COMPLEX1_75K_1 Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. PlfCSekhlspiGaCRmC |
Chain | Residue | Details |
3 | PRO31-CYS48 |
site_id | PS00642 |
Number of Residues | 13 |
Details | COMPLEX1_75K_2 Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. CPtCDkGGaCeLQ |
Chain | Residue | Details |
3 | CYS119-GLN131 |
site_id | PS00643 |
Number of Residues | 11 |
Details | COMPLEX1_75K_3 Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. RCIhCkRCVrY |
Chain | Residue | Details |
3 | ARG180-TYR190 |
site_id | PS00644 |
Number of Residues | 16 |
Details | COMPLEX1_51K_1 Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. GAGAYICGEETALMNS |
Chain | Residue | Details |
1 | GLY176-SER191 |
site_id | PS00645 |
Number of Residues | 12 |
Details | COMPLEX1_51K_2 Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. ESCGkCtPCReG |
Chain | Residue | Details |
1 | GLU351-GLY362 |
site_id | PS01099 |
Number of Residues | 19 |
Details | COMPLEX1_24K Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. DglFSvqkveCLGsChtAP |
Chain | Residue | Details |
2 | ASP114-PRO132 |
site_id | PS01150 |
Number of Residues | 17 |
Details | COMPLEX1_20K Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. NvDSVVPVDVYvPgCPP |
Chain | Residue | Details |
6 | ASN126-PRO142 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 20 |
Details | BINDING: BINDING => ECO:0000269|PubMed:16469879 |
Chain | Residue | Details |
9 | CYS53 | |
9 | CYS108 | |
G | CYS53 | |
G | CYS56 | |
G | SER57 | |
G | CYS59 | |
G | CYS63 | |
G | CYS98 | |
G | ILE99 | |
G | CYS101 | |
G | CYS104 | |
9 | CYS56 | |
G | CYS108 | |
C | CYS256 | |
C | CYS259 | |
C | CYS263 | |
C | CYS291 | |
9 | SER57 | |
9 | CYS59 | |
9 | CYS63 | |
9 | CYS98 | |
9 | ILE99 | |
9 | CYS101 | |
9 | CYS104 |
site_id | SWS_FT_FI2 |
Number of Residues | 2 |
Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU01184, ECO:0000269|PubMed:16469879 |
Chain | Residue | Details |
3 | HIS115 | |
A | ASN92 | |
A | TYR180 | |
A | ILE218 | |
A | CYS353 | |
A | CYS356 | |
A | CYS359 | |
A | CYS400 | |
C | HIS115 | |
1 | TYR180 | |
1 | ILE218 | |
1 | CYS353 | |
1 | CYS356 | |
1 | CYS359 | |
1 | CYS400 | |
A | LYS75 |
site_id | SWS_FT_FI3 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU01184 |
Chain | Residue | Details |
3 | CYS119 | |
3 | CYS122 | |
3 | CYS128 | |
C | CYS119 | |
C | CYS122 | |
C | CYS128 |
Catalytic Information from CSA
site_id | CSA1 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1h2r |
Chain | Residue | Details |
4 | VAL403 |
site_id | CSA2 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1h2r |
Chain | Residue | Details |
D | VAL403 |