Solution NMR structure of the cactus-derived antimicrobial peptide Ep-AMP1
Polymer type: polypeptide(L)
Total | 1H | 13C | |
---|---|---|---|
All | 76.8 % (252 of 328) | 97.9 % (186 of 190) | 47.8 % (66 of 138) |
Backbone | 76.2 % (131 of 172) | 98.6 % (72 of 73) | 59.6 % (59 of 99) |
Sidechain | 79.5 % (147 of 185) | 97.4 % (114 of 117) | 48.5 % (33 of 68) |
Aromatic | 40.0 % (4 of 10) | 80.0 % (4 of 5) | 0.0 % (0 of 5) |
Methyl | 47.1 % (16 of 34) | 88.2 % (15 of 17) | 5.9 % (1 of 17) |
1. Ep-AMP1
CVLIGQRCDN DRGPRCCSGQ GNCVPLPFLG GVCAVSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Ep-AMP1 | natural abundance | 6 mg/mL | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 3.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
4 | Ep-AMP1 | natural abundance | 4 mg/mL | |
5 | D2O | natural abundance | 100 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Ep-AMP1 | natural abundance | 6 mg/mL | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Ep-AMP1 | natural abundance | 6 mg/mL | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Ep-AMP1 | natural abundance | 6 mg/mL | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 3.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
4 | Ep-AMP1 | natural abundance | 4 mg/mL | |
5 | D2O | natural abundance | 100 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 3.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
4 | Ep-AMP1 | natural abundance | 4 mg/mL | |
5 | D2O | natural abundance | 100 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 3.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
4 | Ep-AMP1 | natural abundance | 4 mg/mL | |
5 | D2O | natural abundance | 100 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 3.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
4 | Ep-AMP1 | natural abundance | 4 mg/mL | |
5 | D2O | natural abundance | 100 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_19570_2mfs.nef |
Input source #2: Coordindates | 2mfs.cif |
Diamagnetism of the molecular assembly | True (excluding Oxygen atoms) |
Whether the assembly has a disulfide bond | True (see coordinates for details) |
Whether the assembly has a other bond | None |
Whether the assembly contains a cyclic polymer | None |
Overall data processing status | Warning |
Disulfide bonds
Ptnr_site_1 | Ptnr_site_2 | Redox_state_prediction_1 | Redox_state_prediction_2 | Distance (Å) |
---|---|---|---|---|
A:1:CYS:SG | A:17:CYS:SG | oxidized, CB 40.802 ppm | oxidized, CA 53.495, CB 39.486 ppm | 2.034 |
A:8:CYS:SG | A:23:CYS:SG | oxidized, CA 52.945, CB 48.577 ppm | oxidized, CA 51.888, CB 38.365 ppm | 2.025 |
A:16:CYS:SG | A:33:CYS:SG | oxidized, CA 55.69, CB 39.457 ppm | oxidized, CA 56.391, CB 39.298 ppm | 2.012 |
Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
NoneNon-standard residues
NoneSequence alignments
--------10--------20--------30----- CVLIGQRCDNDRGPRCCSGQGNCVPLPFLGGVCAV ||||||||||||||||||||||||||||||||||| CVLIGQRCDNDRGPRCCSGQGNCVPLPFLGGVCAV
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 35 | 0 | 0 | 100.0 |
Content subtype: combined_19570_2mfs.nef
# | Content subtype | Saveframe | Status | # of rows (sets) | Experiment type | Sequence coverage (%) |
---|---|---|---|---|---|---|
1 | Covalent bonds | assembly | OK | 3 | No information | |
1 | Assigned chemical shifts | assigned_chem_shift_list_1 | OK | 248 | 100.0 (chain: A, length: 35) | |
1 | Distance restraints | CNS/XPLOR_distance_constraints_2 | OK | 456 (1) | noe | 100.0 (chain: A, length: 35) |
2 | Distance restraints | CNS/XPLOR_distance_constraints_3 | OK | 30 (1) | hbond | 57.1 (chain: A, length: 35) |
1 | Dihedral angle restraints | CNS/XPLOR_dihedral_4 | OK | 68 (68) | . | 100.0 (chain: A, length: 35) |
Assigned chemical shifts
--------10--------20--------30----- CVLIGQRCDNDRGPRCCSGQGNCVPLPFLGGVCAV ||||||||||||||||||||||||||||||||||| CVLIGQRCDNDRGPRCCSGQGNCVPLPFLGGVCAV
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 190 | 186 | 97.9 |
13C chemical shifts | 138 | 62 | 44.9 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 73 | 72 | 98.6 |
13C chemical shifts | 70 | 31 | 44.3 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 117 | 114 | 97.4 |
13C chemical shifts | 68 | 31 | 45.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 17 | 15 | 88.2 |
13C chemical shifts | 17 | 1 | 5.9 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 5 | 4 | 80.0 |
13C chemical shifts | 5 | 0 | 0.0 |
Covalent bonds
Distance restraints
--------10--------20--------30----- CVLIGQRCDNDRGPRCCSGQGNCVPLPFLGGVCAV ||||||||||||||||||||||||||||||||||| CVLIGQRCDNDRGPRCCSGQGNCVPLPFLGGVCAV
--------10--------20--------30----- CVLIGQRCDNDRGPRCCSGQGNCVPLPFLGGVCAV ||||| || ||| | | | | | ||||| .VLIGQ.CD...GPR.C..Q.N.V.L...GGVCA --------10--------20--------30----
Dihedral angle restraints
--------10--------20--------30----- CVLIGQRCDNDRGPRCCSGQGNCVPLPFLGGVCAV ||||||||||||||||||||||||||||||||||| CVLIGQRCDNDRGPRCCSGQGNCVPLPFLGGVCAV