6N4I
Structural basis of Nav1.7 inhibition by a gating-modifier spider toxin
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005216 | molecular_function | monoatomic ion channel activity |
| A | 0005261 | molecular_function | monoatomic cation channel activity |
| A | 0005886 | cellular_component | plasma membrane |
| A | 0006811 | biological_process | monoatomic ion transport |
| A | 0016020 | cellular_component | membrane |
| A | 0055085 | biological_process | transmembrane transport |
| B | 0005216 | molecular_function | monoatomic ion channel activity |
| B | 0005261 | molecular_function | monoatomic cation channel activity |
| B | 0005886 | cellular_component | plasma membrane |
| B | 0006811 | biological_process | monoatomic ion transport |
| B | 0016020 | cellular_component | membrane |
| B | 0055085 | biological_process | transmembrane transport |
| C | 0005216 | molecular_function | monoatomic ion channel activity |
| C | 0005261 | molecular_function | monoatomic cation channel activity |
| C | 0005886 | cellular_component | plasma membrane |
| C | 0006811 | biological_process | monoatomic ion transport |
| C | 0016020 | cellular_component | membrane |
| C | 0055085 | biological_process | transmembrane transport |
| D | 0005216 | molecular_function | monoatomic ion channel activity |
| D | 0005261 | molecular_function | monoatomic cation channel activity |
| D | 0005886 | cellular_component | plasma membrane |
| D | 0006811 | biological_process | monoatomic ion transport |
| D | 0016020 | cellular_component | membrane |
| D | 0055085 | biological_process | transmembrane transport |
| E | 0005246 | molecular_function | calcium channel regulator activity |
| E | 0005576 | cellular_component | extracellular region |
| E | 0008289 | molecular_function | lipid binding |
| E | 0017080 | molecular_function | sodium channel regulator activity |
| E | 0035821 | biological_process | modulation of process of another organism |
| E | 0090729 | molecular_function | toxin activity |
| E | 0099106 | molecular_function | ion channel regulator activity |
| F | 0005246 | molecular_function | calcium channel regulator activity |
| F | 0005576 | cellular_component | extracellular region |
| F | 0008289 | molecular_function | lipid binding |
| F | 0017080 | molecular_function | sodium channel regulator activity |
| F | 0035821 | biological_process | modulation of process of another organism |
| F | 0090729 | molecular_function | toxin activity |
| F | 0099106 | molecular_function | ion channel regulator activity |
| G | 0005246 | molecular_function | calcium channel regulator activity |
| G | 0005576 | cellular_component | extracellular region |
| G | 0008289 | molecular_function | lipid binding |
| G | 0017080 | molecular_function | sodium channel regulator activity |
| G | 0035821 | biological_process | modulation of process of another organism |
| G | 0090729 | molecular_function | toxin activity |
| G | 0099106 | molecular_function | ion channel regulator activity |
| H | 0005246 | molecular_function | calcium channel regulator activity |
| H | 0005576 | cellular_component | extracellular region |
| H | 0008289 | molecular_function | lipid binding |
| H | 0017080 | molecular_function | sodium channel regulator activity |
| H | 0035821 | biological_process | modulation of process of another organism |
| H | 0090729 | molecular_function | toxin activity |
| H | 0099106 | molecular_function | ion channel regulator activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 10 |
| Details | binding site for residue 6OU A 1001 |
| Chain | Residue |
| A | MET861 |
| D | PHE927 |
| A | THR862 |
| A | PHE865 |
| A | GLY888 |
| A | GLU889 |
| A | PHE891 |
| B | 6OU1002 |
| D | TRP919 |
| D | ILE923 |
| site_id | AC2 |
| Number of Residues | 1 |
| Details | binding site for residue 6OU A 1002 |
| Chain | Residue |
| A | HIS754 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue 6OU A 1003 |
| Chain | Residue |
| A | LEU875 |
| A | PHE876 |
| A | TYR915 |
| A | TYR917 |
| A | ALA918 |
| B | LEU819 |
| site_id | AC4 |
| Number of Residues | 9 |
| Details | binding site for residue 6OU B 1001 |
| Chain | Residue |
| A | MET912 |
| A | TRP919 |
| A | PHE927 |
| B | MET861 |
| B | THR862 |
| B | GLY888 |
| B | GLU889 |
| B | PHE891 |
| B | TYR892 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | binding site for residue 6OU B 1002 |
| Chain | Residue |
| A | 6OU1001 |
| B | LEU748 |
| B | MET752 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | binding site for residue 6OU B 1003 |
| Chain | Residue |
| B | LEU875 |
| B | PHE876 |
| B | TYR915 |
| B | TYR917 |
| C | LEU819 |
| C | SER820 |
| site_id | AC7 |
| Number of Residues | 9 |
| Details | binding site for residue 6OU C 1001 |
| Chain | Residue |
| B | MET912 |
| B | TRP919 |
| B | PHE927 |
| C | MET861 |
| C | THR862 |
| C | PHE865 |
| C | GLY888 |
| C | GLU889 |
| C | PHE891 |
| site_id | AC8 |
| Number of Residues | 2 |
| Details | binding site for residue 6OU C 1002 |
| Chain | Residue |
| C | MET752 |
| C | HIS754 |
| site_id | AC9 |
| Number of Residues | 8 |
| Details | binding site for residue 6OU D 1001 |
| Chain | Residue |
| C | TRP919 |
| C | PHE927 |
| D | MET861 |
| D | THR862 |
| D | PHE865 |
| D | GLY888 |
| D | GLU889 |
| D | PHE891 |
| site_id | AD1 |
| Number of Residues | 2 |
| Details | binding site for residue 6OU D 1002 |
| Chain | Residue |
| D | MET752 |
| D | HIS754 |
| site_id | AD2 |
| Number of Residues | 3 |
| Details | binding site for residue 6OU D 1003 |
| Chain | Residue |
| C | TYR915 |
| C | PRO916 |
| D | LEU819 |
| site_id | AD3 |
| Number of Residues | 5 |
| Details | binding site for residue 6OU D 1004 |
| Chain | Residue |
| A | LEU819 |
| D | LEU875 |
| D | PHE876 |
| D | TYR915 |
| D | TYR917 |
| site_id | AD4 |
| Number of Residues | 1 |
| Details | binding site for residue 6OU F 101 |
| Chain | Residue |
| F | THR8 |
| site_id | AD5 |
| Number of Residues | 1 |
| Details | binding site for residue 6OU G 101 |
| Chain | Residue |
| G | THR8 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 12 |
| Details | SITE: Part of an aromatic-rich surface that anchors the toxin toward the membrane core relative to lipid headgroups bound along the pore module of Nav1.7/SCN9A => ECO:0000305|PubMed:30661758 |
| Chain | Residue | Details |
| E | TRP5 | |
| H | TRP5 | |
| H | TRP7 | |
| H | TRP30 | |
| E | TRP7 | |
| E | TRP30 | |
| F | TRP5 | |
| F | TRP7 | |
| F | TRP30 | |
| G | TRP5 | |
| G | TRP7 | |
| G | TRP30 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | SITE: Electrostatic gating-modifier of Nav1.7/SCN9A that antagonizes outward gating-charge movement through direct electrostatic repulsion; may also indirectly antagonize S4 gating-charge movement by neutralizing acidic side chains within the extracellular vestibule of VSD2 => ECO:0000305|PubMed:30661758 |
| Chain | Residue | Details |
| E | ARG22 | |
| F | ARG22 | |
| G | ARG22 | |
| H | ARG22 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | SITE: Part of an aromatic-rich surface that anchors the toxin toward the membrane core relative to lipid headgroups bound along the pore module of Nav1.7/SCN9A; it also stabilizes the toxin for productive receptor site engagement => ECO:0000305|PubMed:30661758 |
| Chain | Residue | Details |
| E | TRP24 | |
| F | TRP24 | |
| G | TRP24 | |
| H | TRP24 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | SITE: Antagonizes outward gating-charge movement of Nav1.7/SCN9A through direct electrostatic repulsion; may also indirectly antagonize S4 gating-charge movement by neutralizing acidic side chains within the extracellular vestibule of VSD2 => ECO:0000305|PubMed:30661758 |
| Chain | Residue | Details |
| E | LYS26 | |
| F | LYS26 | |
| G | LYS26 | |
| H | LYS26 |
