Solution structure of the third Immunoglobulin-like domain of nectin-1
LNVQYEPEVT IEGFDGNWYL QRTDVKLTCK ADANPPATEY HWTTLNGSLP KGVEAQNRTL FFRGPITYSL AGTYICEATN PIGTRSGQVE VNITH
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 53.8 % (585 of 1087) | 55.6 % (311 of 559) | 44.6 % (190 of 426) | 82.4 % (84 of 102) |
Backbone | 77.4 % (432 of 558) | 87.0 % (167 of 192) | 65.3 % (181 of 277) | 94.4 % (84 of 89) |
Sidechain | 38.0 % (234 of 616) | 39.2 % (144 of 367) | 38.1 % (90 of 236) | 0.0 % (0 of 13) |
Aromatic | 0.0 % (0 of 102) | 0.0 % (0 of 51) | 0.0 % (0 of 49) | 0.0 % (0 of 2) |
Methyl | 41.7 % (45 of 108) | 63.0 % (34 of 54) | 20.4 % (11 of 54) |
1. entity
LNVQYEPEVT IEGFDGNWYL QRTDVKLTCK ADANPPATEY HWTTLNGSLP KGVEAQNRTL FFRGPITYSL AGTYICEATN PIGTRSGQVE VNITHSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | nectin-1 | [U-13C; U-15N] | 1.0 mM | |
2 | sodium phosphate | natural abundance | 10 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 0.02 % v/v |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | external | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | external | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | external | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | external | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | external | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | external | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | external | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | external | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | external | indirect | 0.1013291 |
Varian INOVA - 750 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | nectin-1 | [U-13C; U-15N] | 1.0 mM | |
2 | sodium phosphate | natural abundance | 10 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 0.02 % v/v |
Varian INOVA - 750 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | nectin-1 | [U-13C; U-15N] | 1.0 mM | |
2 | sodium phosphate | natural abundance | 10 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 0.02 % v/v |
Varian INOVA - 750 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | nectin-1 | [U-13C; U-15N] | 1.0 mM | |
2 | sodium phosphate | natural abundance | 10 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 0.02 % v/v |
Varian INOVA - 750 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | nectin-1 | [U-13C; U-15N] | 1.0 mM | |
2 | sodium phosphate | natural abundance | 10 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 0.02 % v/v |
Varian INOVA - 750 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | nectin-1 | [U-13C; U-15N] | 1.0 mM | |
2 | sodium phosphate | natural abundance | 10 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 0.02 % v/v |
Varian INOVA - 750 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | nectin-1 | [U-13C; U-15N] | 1.0 mM | |
2 | sodium phosphate | natural abundance | 10 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 0.02 % v/v |
Varian INOVA - 750 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | nectin-1 | [U-13C; U-15N] | 1.0 mM | |
2 | sodium phosphate | natural abundance | 10 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 0.02 % v/v |
Varian INOVA - 750 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | nectin-1 | [U-13C; U-15N] | 1.0 mM | |
2 | sodium phosphate | natural abundance | 10 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 0.02 % v/v |
Varian INOVA - 750 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | nectin-1 | [U-13C; U-15N] | 1.0 mM | |
2 | sodium phosphate | natural abundance | 10 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 0.02 % v/v |
Varian INOVA - 750 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | nectin-1 | [U-13C; U-15N] | 1.0 mM | |
2 | sodium phosphate | natural abundance | 10 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 0.02 % v/v |
Varian INOVA - 750 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | nectin-1 | [U-13C; U-15N] | 1.0 mM | |
2 | sodium phosphate | natural abundance | 10 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 0.02 % v/v |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints | combined_17358_2l7j.nef |
Input source #2: Coordindates | 2l7j.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 (Ã…) |
---|---|---|---|---|
A:269:CYS:SG | A:316:CYS:SG | oxidized, CA 55.31, CB 42.28 ppm | oxidized, CA 52.02, CB 44.46 ppm | 2.031 |
Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
NoneNon-standard residues
NoneSequence alignments
-------250-------260-------270-------280-------290-------300-------310-------320-------330----- LNVQYEPEVTIEGFDGNWYLQRTDVKLTCKADANPPATEYHWTTLNGSLPKGVEAQNRTLFFRGPITYSLAGTYICEATNPIGTRSGQVEVNITH ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| LNVQYEPEVTIEGFDGNWYLQRTDVKLTCKADANPPATEYHWTTLNGSLPKGVEAQNRTLFFRGPITYSLAGTYICEATNPIGTRSGQVEVNITH --------10--------20--------30--------40--------50--------60--------70--------80--------90-----
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 95 | 0 | 0 | 100.0 |
Content subtype: combined_17358_2l7j.nef
Assigned chemical shifts
-------250-------260-------270-------280-------290-------300-------310-------320-------330----- LNVQYEPEVTIEGFDGNWYLQRTDVKLTCKADANPPATEYHWTTLNGSLPKGVEAQNRTLFFRGPITYSLAGTYICEATNPIGTRSGQVEVNITH |||||||||||| || |||||||||||||||||| |||||||||||||||| |||| ||||||||||| |||||||||||||||||||||||||| LNVQYEPEVTIE.FD.NWYLQRTDVKLTCKADAN.PATEYHWTTLNGSLPK.VEAQ.RTLFFRGPITY.LAGTYICEATNPIGTRSGQVEVNITH
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 559 | 306 | 54.7 |
13C chemical shifts | 426 | 170 | 39.9 |
15N chemical shifts | 106 | 84 | 79.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 192 | 167 | 87.0 |
13C chemical shifts | 190 | 89 | 46.8 |
15N chemical shifts | 89 | 84 | 94.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 367 | 139 | 37.9 |
13C chemical shifts | 236 | 81 | 34.3 |
15N chemical shifts | 17 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 54 | 33 | 61.1 |
13C chemical shifts | 54 | 6 | 11.1 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 51 | 0 | 0.0 |
13C chemical shifts | 49 | 0 | 0.0 |
15N chemical shifts | 2 | 0 | 0.0 |
Covalent bonds
Distance restraints
-------250-------260-------270-------280-------290-------300-------310-------320-------330----- LNVQYEPEVTIEGFDGNWYLQRTDVKLTCKADANPPATEYHWTTLNGSLPKGVEAQNRTLFFRGPITYSLAGTYICEATNPIGTRSGQVEVNITH ||||||||||| || |||||||||||||||||| ||||||||||||| || |||| |||||||||| |||||||||||||||||||||||||| .NVQYEPEVTIE.FD.NWYLQRTDVKLTCKADAN.PATEYHWTTLNGS.PK.VEAQ..TLFFRGPITY.LAGTYICEATNPIGTRSGQVEVNITH