5KK4
Crystal Structure of the Plant Defensin NsD7 bound to Phosphatidic Acid
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005773 | cellular_component | vacuole |
| A | 0006952 | biological_process | defense response |
| A | 0008289 | molecular_function | lipid binding |
| A | 0031640 | biological_process | killing of cells of another organism |
| A | 0070300 | molecular_function | phosphatidic acid binding |
| B | 0005773 | cellular_component | vacuole |
| B | 0006952 | biological_process | defense response |
| B | 0008289 | molecular_function | lipid binding |
| B | 0031640 | biological_process | killing of cells of another organism |
| B | 0070300 | molecular_function | phosphatidic acid binding |
| C | 0005773 | cellular_component | vacuole |
| C | 0006952 | biological_process | defense response |
| C | 0008289 | molecular_function | lipid binding |
| C | 0031640 | biological_process | killing of cells of another organism |
| C | 0070300 | molecular_function | phosphatidic acid binding |
| D | 0005773 | cellular_component | vacuole |
| D | 0006952 | biological_process | defense response |
| D | 0008289 | molecular_function | lipid binding |
| D | 0031640 | biological_process | killing of cells of another organism |
| D | 0070300 | molecular_function | phosphatidic acid binding |
| E | 0005773 | cellular_component | vacuole |
| E | 0006952 | biological_process | defense response |
| E | 0008289 | molecular_function | lipid binding |
| E | 0031640 | biological_process | killing of cells of another organism |
| E | 0070300 | molecular_function | phosphatidic acid binding |
| F | 0005773 | cellular_component | vacuole |
| F | 0006952 | biological_process | defense response |
| F | 0008289 | molecular_function | lipid binding |
| F | 0031640 | biological_process | killing of cells of another organism |
| F | 0070300 | molecular_function | phosphatidic acid binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 101 |
| Chain | Residue |
| A | GLY12 |
| A | ILE13 |
| A | HOH228 |
| A | HOH238 |
| E | EDO101 |
| site_id | AC2 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 102 |
| Chain | Residue |
| A | THR16 |
| F | EDO104 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 A 103 |
| Chain | Residue |
| C | PRO11 |
| C | GLY12 |
| A | LYS1 |
| A | HOH215 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue ACT A 104 |
| Chain | Residue |
| A | SER35 |
| A | LYS36 |
| A | ILE37 |
| A | LEU38 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 B 101 |
| Chain | Residue |
| B | PRO11 |
| B | GLY12 |
| B | EDO103 |
| C | HOH216 |
| D | 44E102 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 102 |
| Chain | Residue |
| B | PHE10 |
| B | PRO11 |
| B | PRO19 |
| B | LYS22 |
| B | HOH234 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 103 |
| Chain | Residue |
| B | SO4101 |
| C | EDO103 |
| C | EDO105 |
| D | 44E102 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | binding site for residue ACT B 104 |
| Chain | Residue |
| B | LYS28 |
| F | LYS45 |
| F | PRO46 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 B 105 |
| Chain | Residue |
| B | ILE15 |
| B | THR16 |
| B | LYS17 |
| B | HOH219 |
| C | LYS36 |
| site_id | AD1 |
| Number of Residues | 12 |
| Details | binding site for residue 44E C 101 |
| Chain | Residue |
| B | LYS36 |
| B | ARG39 |
| B | HOH215 |
| C | ILE15 |
| C | THR16 |
| C | LYS17 |
| C | HIS33 |
| C | CYS34 |
| C | LYS36 |
| C | ARG39 |
| C | HOH201 |
| F | HOH240 |
| site_id | AD2 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 C 102 |
| Chain | Residue |
| C | LYS4 |
| C | HIS33 |
| C | LEU42 |
| C | HOH219 |
| site_id | AD3 |
| Number of Residues | 8 |
| Details | binding site for residue EDO C 103 |
| Chain | Residue |
| B | ILE13 |
| B | EDO103 |
| C | SER35 |
| C | LYS36 |
| C | ILE37 |
| C | LEU38 |
| C | EDO105 |
| C | HOH219 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue ACT C 104 |
| Chain | Residue |
| C | GLY12 |
| C | ILE13 |
| C | HOH207 |
| F | ILE15 |
| site_id | AD5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 105 |
| Chain | Residue |
| B | EDO103 |
| C | SER35 |
| C | ARG40 |
| C | EDO103 |
| C | HOH216 |
| site_id | AD6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 106 |
| Chain | Residue |
| C | LYS4 |
| D | LEU42 |
| D | 44E102 |
| site_id | AD7 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 101 |
| Chain | Residue |
| A | PRO46 |
| A | HOH240 |
| D | ARG21 |
| D | ILE25 |
| D | EDO107 |
| D | HOH210 |
| site_id | AD8 |
| Number of Residues | 12 |
| Details | binding site for residue 44E D 102 |
| Chain | Residue |
| B | SO4101 |
| B | EDO103 |
| B | HOH233 |
| C | EDO106 |
| D | LYS4 |
| D | HIS33 |
| D | SER35 |
| D | LYS36 |
| D | ILE37 |
| D | LEU38 |
| D | LEU42 |
| E | ILE15 |
| site_id | AD9 |
| Number of Residues | 12 |
| Details | binding site for residue 44E D 103 |
| Chain | Residue |
| D | EDO106 |
| D | HOH215 |
| E | LYS36 |
| E | ARG39 |
| D | ILE15 |
| D | THR16 |
| D | LYS17 |
| D | PRO18 |
| D | HIS33 |
| D | CYS34 |
| D | LYS36 |
| D | ARG39 |
| site_id | AE1 |
| Number of Residues | 5 |
| Details | binding site for residue EDO D 105 |
| Chain | Residue |
| C | LYS1 |
| D | GLU6 |
| D | ASN8 |
| D | HOH202 |
| F | ALA0 |
| site_id | AE2 |
| Number of Residues | 5 |
| Details | binding site for residue EDO D 106 |
| Chain | Residue |
| D | PRO18 |
| D | ARG21 |
| D | 44E103 |
| D | HOH201 |
| D | HOH206 |
| site_id | AE3 |
| Number of Residues | 3 |
| Details | binding site for residue EDO D 107 |
| Chain | Residue |
| D | LYS22 |
| D | EDO101 |
| D | HOH206 |
| site_id | AE4 |
| Number of Residues | 8 |
| Details | binding site for residue EDO E 101 |
| Chain | Residue |
| A | EDO101 |
| A | HOH228 |
| E | SER35 |
| E | LYS36 |
| E | ILE37 |
| E | LEU38 |
| E | 44E102 |
| E | HOH201 |
| site_id | AE5 |
| Number of Residues | 12 |
| Details | binding site for residue 44E E 102 |
| Chain | Residue |
| A | THR9 |
| A | PRO11 |
| A | GLY12 |
| E | LYS1 |
| E | LYS4 |
| E | HIS33 |
| E | SER35 |
| E | LEU42 |
| E | EDO101 |
| E | HOH201 |
| F | ARG40 |
| F | HOH201 |
| site_id | AE6 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 E 103 |
| Chain | Residue |
| D | LYS36 |
| D | HOH215 |
| E | THR16 |
| E | LYS17 |
| E | PRO18 |
| E | HOH204 |
| site_id | AE7 |
| Number of Residues | 9 |
| Details | binding site for residue 44E F 101 |
| Chain | Residue |
| B | HIS33 |
| B | SER35 |
| B | LYS36 |
| B | ILE37 |
| B | LEU42 |
| B | HOH237 |
| C | ILE15 |
| F | GLY12 |
| F | ILE13 |
| site_id | AE8 |
| Number of Residues | 12 |
| Details | binding site for residue 44E F 102 |
| Chain | Residue |
| A | LYS36 |
| A | ARG39 |
| A | HOH211 |
| F | THR16 |
| F | LYS17 |
| F | HIS33 |
| F | CYS34 |
| F | LYS36 |
| F | ARG39 |
| F | HOH210 |
| F | HOH230 |
| F | HOH239 |
| site_id | AE9 |
| Number of Residues | 2 |
| Details | binding site for residue EDO F 103 |
| Chain | Residue |
| F | LYS22 |
| F | HOH208 |
| site_id | AF1 |
| Number of Residues | 2 |
| Details | binding site for residue EDO F 104 |
| Chain | Residue |
| A | EDO102 |
| F | EDO106 |
| site_id | AF2 |
| Number of Residues | 4 |
| Details | binding site for residue EDO F 105 |
| Chain | Residue |
| F | LYS4 |
| F | HIS33 |
| F | HOH224 |
| F | HOH230 |
| site_id | AF3 |
| Number of Residues | 4 |
| Details | binding site for residue EDO F 106 |
| Chain | Residue |
| F | SER35 |
| F | ILE37 |
| F | LEU38 |
| F | EDO104 |
Functional Information from PROSITE/UniProt
| site_id | PS00940 |
| Number of Residues | 24 |
| Details | GAMMA_THIONIN Gamma-thionins family signature. KdCkreSntFp.GiCitkppCrkaC |
| Chain | Residue | Details |
| A | LYS1-CYS24 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 24 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:27647905 |
| Chain | Residue | Details |
| A | LYS4 | |
| C | HIS33 | |
| C | LYS36 | |
| C | ARG39 | |
| D | LYS4 | |
| D | HIS33 | |
| D | LYS36 | |
| D | ARG39 | |
| E | LYS4 | |
| E | HIS33 | |
| E | LYS36 | |
| A | HIS33 | |
| E | ARG39 | |
| F | LYS4 | |
| F | HIS33 | |
| F | LYS36 | |
| F | ARG39 | |
| A | LYS36 | |
| A | ARG39 | |
| B | LYS4 | |
| B | HIS33 | |
| B | LYS36 | |
| B | ARG39 | |
| C | LYS4 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 12 |
| Details | SITE: Required for formation of double helix => ECO:0000269|PubMed:27647905 |
| Chain | Residue | Details |
| A | ILE15 | |
| E | ILE37 | |
| F | ILE15 | |
| F | ILE37 | |
| A | ILE37 | |
| B | ILE15 | |
| B | ILE37 | |
| C | ILE15 | |
| C | ILE37 | |
| D | ILE15 | |
| D | ILE37 | |
| E | ILE15 |
