NMR structure of the lymphocyte receptor NKR-P1A
SAKLECPQDW LSHRDKCFHV SQVSNTWEEG LVDCDGKGAT LMLIQDQEEL RFLLDSIKEK YNSFWIGLRY TLPDMNWKWI NGSTLNSDVL KITGDTENDS CAAISGDKVT FESCNSDNRW ICQKELYHET LSNYVGYGH
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 98.6 % (1602 of 1624) | 98.1 % (824 of 840) | 99.4 % (623 of 627) | 98.7 % (155 of 157) |
Backbone | 98.7 % (819 of 830) | 97.5 % (278 of 285) | 99.5 % (406 of 408) | 98.5 % (135 of 137) |
Sidechain | 98.8 % (913 of 924) | 98.4 % (546 of 555) | 99.4 % (347 of 349) | 100.0 % (20 of 20) |
Aromatic | 97.6 % (164 of 168) | 97.6 % (82 of 84) | 97.4 % (76 of 78) | 100.0 % (6 of 6) |
Methyl | 100.0 % (132 of 132) | 100.0 % (66 of 66) | 100.0 % (66 of 66) |
1. NKR-P1A
SAKLECPQDW LSHRDKCFHV SQVSNTWEEG LVDCDGKGAT LMLIQDQEEL RFLLDSIKEK YNSFWIGLRY TLPDMNWKWI NGSTLNSDVL KITGDTENDS CAAISGDKVT FESCNSDNRW ICQKELYHET LSNYVGYGHSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | NKR-P1A | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PIPES | natural abundance | 15 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | NKR-P1A | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PIPES | natural abundance | 15 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | NKR-P1A | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PIPES | natural abundance | 15 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | NKR-P1A | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PIPES | natural abundance | 15 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | NKR-P1A | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PIPES | natural abundance | 15 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | NKR-P1A | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PIPES | natural abundance | 15 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | NKR-P1A | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PIPES | natural abundance | 15 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | NKR-P1A | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PIPES | natural abundance | 15 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | NKR-P1A | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PIPES | natural abundance | 15 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | NKR-P1A | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PIPES | natural abundance | 15 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | NKR-P1A | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PIPES | natural abundance | 15 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | NKR-P1A | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PIPES | natural abundance | 15 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | NKR-P1A | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PIPES | natural abundance | 15 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | NKR-P1A | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PIPES | natural abundance | 15 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | NKR-P1A | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PIPES | natural abundance | 15 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | NKR-P1A | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PIPES | natural abundance | 15 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | NKR-P1A | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PIPES | natural abundance | 15 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | NKR-P1A | [U-100% 13C; U-100% 15N] | 0.5 mM | |
2 | PIPES | natural abundance | 15 mM | |
3 | sodium chloride | natural abundance | 50 mM | |
4 | sodium azide | natural abundance | 1 mM | |
5 | H2O | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_19282_2mti.nef |
Input source #2: Coordindates | 2mti.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:6:CYS:SG | A:17:CYS:SG | oxidized, CA 53.218, CB 37.445 ppm | oxidized, CA 52.547, CB 43.197 ppm | 2.002 |
A:34:CYS:SG | A:122:CYS:SG | oxidized, CA 56.07, CB 34.421 ppm | oxidized, CA 51.576, CB 39.418 ppm | 2.026 |
A:101:CYS:SG | A:114:CYS:SG | oxidized, CA 59.446, CB 45.631 ppm | oxidized, CA 59.652, CB 45.624 ppm | 2.023 |
Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
NoneNon-standard residues
NoneSequence alignments
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 SAKLECPQDWLSHRDKCFHVSQVSNTWEEGLVDCDGKGATLMLIQDQEELRFLLDSIKEKYNSFWIGLRYTLPDMNWKWINGSTLNSDVLKITGDTENDS |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| SAKLECPQDWLSHRDKCFHVSQVSNTWEEGLVDCDGKGATLMLIQDQEELRFLLDSIKEKYNSFWIGLRYTLPDMNWKWINGSTLNSDVLKITGDTENDS -------110-------120-------130--------- CAAISGDKVTFESCNSDNRWICQKELYHETLSNYVGYGH ||||||||||||||||||||||||||||||||||||||| CAAISGDKVTFESCNSDNRWICQKELYHETLSNYVGYGH
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 139 | 0 | 0 | 100.0 |
Content subtype: combined_19282_2mti.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 SAKLECPQDWLSHRDKCFHVSQVSNTWEEGLVDCDGKGATLMLIQDQEELRFLLDSIKEKYNSFWIGLRYTLPDMNWKWINGSTLNSDVLKITGDTENDS ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| .AKLECPQDWLSHRDKCFHVSQVSNTWEEGLVDCDGKGATLMLIQDQEELRFLLDSIKEKYNSFWIGLRYTLPDMNWKWINGSTLNSDVLKITGDTENDS -------110-------120-------130--------- CAAISGDKVTFESCNSDNRWICQKELYHETLSNYVGYGH ||||||||||||||||||||||||||||||||||||||| CAAISGDKVTFESCNSDNRWICQKELYHETLSNYVGYGH
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 840 | 831 | 98.9 |
13C chemical shifts | 627 | 622 | 99.2 |
15N chemical shifts | 161 | 157 | 97.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 285 | 281 | 98.6 |
13C chemical shifts | 278 | 276 | 99.3 |
15N chemical shifts | 137 | 134 | 97.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 555 | 550 | 99.1 |
13C chemical shifts | 349 | 346 | 99.1 |
15N chemical shifts | 24 | 23 | 95.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 68 | 68 | 100.0 |
13C chemical shifts | 68 | 68 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 84 | 82 | 97.6 |
13C chemical shifts | 78 | 76 | 97.4 |
15N chemical shifts | 6 | 6 | 100.0 |
Covalent bonds
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 SAKLECPQDWLSHRDKCFHVSQVSNTWEEGLVDCDGKGATLMLIQDQEELRFLLDSIKEKYNSFWIGLRYTLPDMNWKWINGSTLNSDVLKITGDTENDS ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| .AKLECPQDWLSHRDKCFHVSQVSNTWEEGLVDCDGKGATLMLIQDQEELRFLLDSIKEKYNSFWIGLRYTLPDMNWKWINGSTLNSDVLKITGDTENDS -------110-------120-------130--------- CAAISGDKVTFESCNSDNRWICQKELYHETLSNYVGYGH ||||||||||||||||||||||||||||||| ||||| | CAAISGDKVTFESCNSDNRWICQKELYHETL.NYVGY.H
Dihedral angle restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 SAKLECPQDWLSHRDKCFHVSQVSNTWEEGLVDCDGKGATLMLIQDQEELRFLLDSIKEKYNSFWIGLRYTLPDMNWKWINGSTLNSDVLKITGDTENDS |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| |||| ...LECPQDWLSHRDKCFHVSQVSNTWEEGLVDCDGKGATL.LIQDQEELRFLLDSIKEKYNSFWIGLRYTLPDMNWKWINGSTLNSDVLKITG..ENDS --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 -------110-------120-------130--------- CAAISGDKVTFESCNSDNRWICQKELYHETLSNYVGYGH ||||||||||||||||| |||||||| || | | | CAAISGDKVTFESCNSD.RWICQKEL..ET..N.V.Y -------110-------120-------130-------