Microvirin:mannobiose complex
MPNFSHTCSS INYDPDSTIL SAECQARDGE WLPTELRLSD HIGNIDGELQ FGDQNFQETC QDCRLEFGDG EQSVWLVCTC QTMDGEWKST QILLDSQIDN NDSQLEIG
ID | Type | Value order | Atom ID 1 | Atom ID 2 |
---|---|---|---|---|
1 | disulfide | sing | 1:CYS8:SG | 1:CYS24:SG |
2 | disulfide | sing | 1:CYS60:SG | 1:CYS80:SG |
3 | disulfide | sing | 1:CYS63:SG | 1:CYS78:SG |
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 65.5 % (793 of 1210) | 44.8 % (281 of 627) | 85.4 % (392 of 459) | 96.8 % (120 of 124) |
Backbone | 95.2 % (611 of 642) | 89.1 % (197 of 221) | 98.4 % (311 of 316) | 98.1 % (103 of 105) |
Sidechain | 42.2 % (282 of 668) | 20.7 % (84 of 406) | 74.5 % (181 of 243) | 89.5 % (17 of 19) |
Aromatic | 33.7 % (31 of 92) | 43.5 % (20 of 46) | 18.6 % (8 of 43) | 100.0 % (3 of 3) |
Methyl | 48.9 % (46 of 94) | 48.9 % (23 of 47) | 48.9 % (23 of 47) |
1. microvirin
MPNFSHTCSS INYDPDSTIL SAECQARDGE WLPTELRLSD HIGNIDGELQ FGDQNFQETC QDCRLEFGDG EQSVWLVCTC QTMDGEWKST QILLDSQIDN NDSQLEIGSolvent system 10% water/90% D2O, Pressure 1.000 atm, Temperature 300.000 K, pH 6.800, Details microvirin 1.5 mM, mannobiose 1.5 mM
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | microvirin | [U-13C; U-15N] | 1.5 mM | |
2 | mannobiose | [U-13C; U-15N] | 1.5 mM | |
3 | H2O | natural abundance | 10 % | |
4 | D2O | natural abundance | 90 % | |
5 | NaPO4 | natural abundance | 20 mM | |
6 | NaCl | natural abundance | 50 mM |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
1H | HDO | HDO | 4.7 ppm | internal | direct | 1.0 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
1H | HDO | HDO | 4.7 ppm | internal | direct | 1.0 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
1H | HDO | HDO | 4.7 ppm | internal | direct | 1.0 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
1H | HDO | HDO | 4.7 ppm | internal | direct | 1.0 |
Bruker Avance - 500 MHz
State isotropic, Solvent system 10% water/90% D2O, Pressure 1.000 atm, Temperature 300.000 K, pH 6.800, Details microvirin 1.5 mM, mannobiose 1.5 mM
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | microvirin | [U-13C; U-15N] | 1.5 mM | |
2 | mannobiose | [U-13C; U-15N] | 1.5 mM | |
3 | H2O | natural abundance | 10 % | |
4 | D2O | natural abundance | 90 % | |
5 | NaPO4 | natural abundance | 20 mM | |
6 | NaCl | natural abundance | 50 mM |
Bruker Avance - 500 MHz
State isotropic, Solvent system 10% water/90% D2O, Pressure 1.000 atm, Temperature 300.000 K, pH 6.800, Details microvirin 1.5 mM, mannobiose 1.5 mM
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | microvirin | [U-13C; U-15N] | 1.5 mM | |
2 | mannobiose | [U-13C; U-15N] | 1.5 mM | |
3 | H2O | natural abundance | 10 % | |
4 | D2O | natural abundance | 90 % | |
5 | NaPO4 | natural abundance | 20 mM | |
6 | NaCl | natural abundance | 50 mM |
Bruker Avance - 500 MHz
State isotropic, Solvent system 10% water/90% D2O, Pressure 1.000 atm, Temperature 300.000 K, pH 6.800, Details microvirin 1.5 mM, mannobiose 1.5 mM
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | microvirin | [U-13C; U-15N] | 1.5 mM | |
2 | mannobiose | [U-13C; U-15N] | 1.5 mM | |
3 | H2O | natural abundance | 10 % | |
4 | D2O | natural abundance | 90 % | |
5 | NaPO4 | natural abundance | 20 mM | |
6 | NaCl | natural abundance | 50 mM |
Bruker Avance - 500 MHz
State isotropic, Solvent system 10% water/90% D2O, Pressure 1.000 atm, Temperature 300.000 K, pH 6.800, Details microvirin 1.5 mM, mannobiose 1.5 mM
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | microvirin | [U-13C; U-15N] | 1.5 mM | |
2 | mannobiose | [U-13C; U-15N] | 1.5 mM | |
3 | H2O | natural abundance | 10 % | |
4 | D2O | natural abundance | 90 % | |
5 | NaPO4 | natural abundance | 20 mM | |
6 | NaCl | natural abundance | 50 mM |
Bruker Avance - 500 MHz
State isotropic, Solvent system 10% water/90% D2O, Pressure 1.000 atm, Temperature 300.000 K, pH 6.800, Details microvirin 1.5 mM, mannobiose 1.5 mM
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | microvirin | [U-13C; U-15N] | 1.5 mM | |
2 | mannobiose | [U-13C; U-15N] | 1.5 mM | |
3 | H2O | natural abundance | 10 % | |
4 | D2O | natural abundance | 90 % | |
5 | NaPO4 | natural abundance | 20 mM | |
6 | NaCl | natural abundance | 50 mM |
Bruker Avance - 500 MHz
State isotropic, Solvent system 10% water/90% D2O, Pressure 1.000 atm, Temperature 300.000 K, pH 6.800, Details microvirin 1.5 mM, mannobiose 1.5 mM
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | microvirin | [U-13C; U-15N] | 1.5 mM | |
2 | mannobiose | [U-13C; U-15N] | 1.5 mM | |
3 | H2O | natural abundance | 10 % | |
4 | D2O | natural abundance | 90 % | |
5 | NaPO4 | natural abundance | 20 mM | |
6 | NaCl | natural abundance | 50 mM |
Bruker Avance - 500 MHz
State isotropic, Solvent system 10% water/90% D2O, Pressure 1.000 atm, Temperature 300.000 K, pH 6.800, Details microvirin 1.5 mM, mannobiose 1.5 mM
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | microvirin | [U-13C; U-15N] | 1.5 mM | |
2 | mannobiose | [U-13C; U-15N] | 1.5 mM | |
3 | H2O | natural abundance | 10 % | |
4 | D2O | natural abundance | 90 % | |
5 | NaPO4 | natural abundance | 20 mM | |
6 | NaCl | natural abundance | 50 mM |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_17625_2yhh.nef |
Input source #2: Coordindates | 2yhh.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 | Error |
Disulfide bonds
Ptnr_site_1 | Ptnr_site_2 | Redox_state_prediction_1 | Redox_state_prediction_2 | Distance (Å) |
---|---|---|---|---|
A:8:CYS:SG | A:24:CYS:SG | oxidized, CA 59.0, CB 46.92 ppm | oxidized, CA 54.2, CB 47.22 ppm | 2.021 |
A:60:CYS:SG | A:80:CYS:SG | oxidized, CA 56.94, CB 50.27 ppm | oxidized, CA 56.46, CB 45.37 ppm | 2.02 |
A:63:CYS:SG | A:78:CYS:SG | oxidized, CA 56.68, CB 44.28 ppm | oxidized, CA 54.8, CB 53.58 ppm | 2.027 |
Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
NoneNon-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
B | 1 | MAN | alpha-D-mannopyranose | Distance restraints, Torsion angle restraints, Coordinates |
B | 2 | MAN | alpha-D-mannopyranose | Coordinates |
Sequence alignments
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MPNFSHTCSSINYDPDSTILSAECQARDGEWLPTELRLSDHIGNIDGELQFGDQNFQETCQDCRLEFGDGEQSVWLVCTCQTMDGEWKSTQILLDSQIDN |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MPNFSHTCSSINYDPDSTILSAECQARDGEWLPTELRLSDHIGNIDGELQFGDQNFQETCQDCRLEFGDGEQSVWLVCTCQTMDGEWKSTQILLDSQIDN -------- NDSQLEIG |||||||| NDSQLEIG
-- XX || XX
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 108 | 0 | 0 | 100.0 |
B | B | 2 | 0 | 0 | 100.0 |
Content subtype: combined_17625_2yhh.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 MPNFSHTCSSINYDPDSTILSAECQARDGEWLPTELRLSDHIGNIDGELQFGDQNFQETCQDCRLEFGDGEQSVWLVCTCQTMDGEWKSTQILLDSQIDN |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MPNFSHTCSSINYDPDSTILSAECQARDGEWLPTELRLSDHIGNIDGELQFGDQNFQETCQDCRLEFGDGEQSVWLVCTCQTMDGEWKSTQILLDSQIDN -------- NDSQLEIG |||||||| NDSQLEIG
Comp_index_ID | Comp_ID | Atom_ID | CS value (ppm) |
---|---|---|---|
41 | HIS | HD1 | 7.324 |
41 | HIS | HE2 | 7.054 |
44 | ASN | CG | 176.8 |
55 | ASN | CG | 178.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 627 | 272 | 43.4 |
13C chemical shifts | 459 | 395 | 86.1 |
15N chemical shifts | 127 | 121 | 95.3 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 221 | 201 | 91.0 |
13C chemical shifts | 216 | 214 | 99.1 |
15N chemical shifts | 105 | 102 | 97.1 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 406 | 71 | 17.5 |
13C chemical shifts | 243 | 181 | 74.5 |
15N chemical shifts | 22 | 19 | 86.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 49 | 24 | 49.0 |
13C chemical shifts | 49 | 24 | 49.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 46 | 20 | 43.5 |
13C chemical shifts | 43 | 8 | 18.6 |
15N chemical shifts | 3 | 3 | 100.0 |
Distance restraints
-- XX | X -
-- XX | X -
Dihedral angle restraints