Structure of SDF-1/CXCL12
ID | Type | Value order | Atom ID 1 | Atom ID 2 |
---|---|---|---|---|
1 | disulfide | sing | 1:CYS11:SG | 1:CYS36:SG |
2 | disulfide | sing | 1:CYS13:SG | 1:CYS52:SG |
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 93.6 % (817 of 873) | 94.0 % (435 of 463) | 92.8 % (309 of 333) | 94.8 % (73 of 77) |
Backbone | 94.2 % (388 of 412) | 92.7 % (127 of 137) | 95.2 % (199 of 209) | 93.9 % (62 of 66) |
Sidechain | 93.8 % (497 of 530) | 94.5 % (308 of 326) | 92.2 % (178 of 193) | 100.0 % (11 of 11) |
Aromatic | 89.3 % (50 of 56) | 100.0 % (28 of 28) | 77.8 % (21 of 27) | 100.0 % (1 of 1) |
Methyl | 92.5 % (74 of 80) | 100.0 % (40 of 40) | 85.0 % (34 of 40) |
1. CXCL12/SDF1-alpha
GMKPVSLSYR CPCRFFESHV ARANVKHLKI LNTPNCALQI VARLKNNNRQ VCIDPKLKWI QEYLEKALNKSolvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 1.56 mM CXCL12 U-15N/13C pH 5.5 50mM sodium phosphate 20 mM MES
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CXCL12/SDF1-alpha | [U-100% 13C; U-100% 15N] | 1.56 mM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % | |
4 | sodium phosphate | natural abundance | 50 mM | |
5 | MES | natural abundance | 20 mM |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | null | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | null | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | null | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | null | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | null | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | null | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | null | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | null | indirect | 0.1013291 |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 1.56 mM CXCL12 U-15N/13C pH 5.5 50mM sodium phosphate 20 mM MES
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CXCL12/SDF1-alpha | [U-100% 13C; U-100% 15N] | 1.56 mM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % | |
4 | sodium phosphate | natural abundance | 50 mM | |
5 | MES | natural abundance | 20 mM |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 1.56 mM CXCL12 U-15N/13C pH 5.5 50mM sodium phosphate 20 mM MES
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CXCL12/SDF1-alpha | [U-100% 13C; U-100% 15N] | 1.56 mM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % | |
4 | sodium phosphate | natural abundance | 50 mM | |
5 | MES | natural abundance | 20 mM |
Bruker Avance - 600 MHz
State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 1.56 mM CXCL12 U-15N/13C pH 5.5 50mM sodium phosphate 20 mM MES
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | CXCL12/SDF1-alpha | [U-100% 13C; U-100% 15N] | 1.56 mM | |
2 | H2O | natural abundance | 90 % | |
3 | D2O | natural abundance | 10 % | |
4 | sodium phosphate | natural abundance | 50 mM | |
5 | MES | natural abundance | 20 mM |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_16142_2kec.nef |
Input source #2: Coordindates | 2kec.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:9:CYS:SG | A:34:CYS:SG | oxidized, CA 53.127, CB 40.218 ppm | oxidized, CA 54.622, CB 44.78 ppm | 2.022 |
A:11:CYS:SG | A:50:CYS:SG | oxidized, CA 53.429, CB 39.603 ppm | oxidized, CA 56.377, CB 44.694 ppm | 2.021 |
Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
NoneNon-standard residues
NoneSequence alignments
-0--------10--------20--------30--------40--------50--------60-------- GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQEYLEKALNK |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQEYLEKALNK --------10--------20--------30--------40--------50--------60--------70
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 70 | 0 | 0 | 100.0 |
Content subtype: combined_16142_2kec.nef
Assigned chemical shifts
-0--------10--------20--------30--------40--------50--------60-------- GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQEYLEKALNK |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ..KPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQEYLEKALNK
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 463 | 447 | 96.5 |
13C chemical shifts | 333 | 307 | 92.2 |
15N chemical shifts | 82 | 73 | 89.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 137 | 131 | 95.6 |
13C chemical shifts | 140 | 132 | 94.3 |
15N chemical shifts | 66 | 62 | 93.9 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 326 | 316 | 96.9 |
13C chemical shifts | 193 | 175 | 90.7 |
15N chemical shifts | 16 | 11 | 68.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 41 | 40 | 97.6 |
13C chemical shifts | 41 | 33 | 80.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 28 | 28 | 100.0 |
13C chemical shifts | 27 | 19 | 70.4 |
15N chemical shifts | 1 | 1 | 100.0 |
Covalent bonds
Distance restraints
-0--------10--------20--------30--------40--------50--------60-------- GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQEYLEKALNK |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ..KPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQEYLEKALNK
Dihedral angle restraints
-0--------10--------20--------30--------40--------50--------60-------- GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQEYLEKALNK ||||||||| ||||| |||||||||||||||||||||||||||||| |||||||||||| .........RCPCRFFES.VARAN.KHLKILNTPNCALQIVARLKNNNRQVCIDP..KWIQEYLEKALN -0--------10--------20--------30--------40--------50--------60-------