NMR Structure of KDM5B PHD1 finger
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 83.1 % (506 of 609) | 83.1 % (261 of 314) | 80.5 % (194 of 241) | 94.4 % (51 of 54) |
Backbone | 95.7 % (308 of 322) | 95.5 % (105 of 110) | 95.0 % (153 of 161) | 98.0 % (50 of 51) |
Sidechain | 73.4 % (248 of 338) | 76.5 % (156 of 204) | 69.5 % (91 of 131) | 33.3 % (1 of 3) |
Aromatic | 39.1 % (18 of 46) | 78.3 % (18 of 23) | 0.0 % (0 of 22) | 0.0 % (0 of 1) |
Methyl | 79.3 % (46 of 58) | 79.3 % (23 of 29) | 79.3 % (23 of 29) |
1. PHD1 finger of KDM5B
AVDLYVCLLC GSGNDEDRLL LCDGCDDSYH TFCLIPPLHD VPKGDWRCPK CLAQESolvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details 50mM phosphate buffer NA; 90% H2O, 10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PHD1 finger of KDM5B | [U-13C; U-15N] | 0.8 mM | |
2 | Phosphate buffer | natural abundance | 50 mM | |
3 | D2O | natural abundance | 10 % | |
4 | H2O | natural abundance | 90 % |
Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details 50mM phosphate buffer NA; 100% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
5 | PHD1 finger of KDM5B | [U-13C; U-15N] | 0.8 mM | |
6 | Phosphate buffer | natural abundance | 50 mM | |
7 | D2O | natural abundance | 100 % |
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 |
31P | DSS | methyl protons | 0.0 ppm | na | indirect | 0.4048086 |
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 |
31P | DSS | methyl protons | 0.0 ppm | na | indirect | 0.4048086 |
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 |
31P | DSS | methyl protons | 0.0 ppm | na | indirect | 0.4048086 |
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 |
31P | DSS | methyl protons | 0.0 ppm | na | indirect | 0.4048086 |
Agilent DD2 - 600 MHz
State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details 50mM phosphate buffer NA; 90% H2O, 10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PHD1 finger of KDM5B | [U-13C; U-15N] | 0.8 mM | |
2 | Phosphate buffer | natural abundance | 50 mM | |
3 | D2O | natural abundance | 10 % | |
4 | H2O | natural abundance | 90 % |
Agilent DD2 - 600 MHz
State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details 50mM phosphate buffer NA; 90% H2O, 10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PHD1 finger of KDM5B | [U-13C; U-15N] | 0.8 mM | |
2 | Phosphate buffer | natural abundance | 50 mM | |
3 | D2O | natural abundance | 10 % | |
4 | H2O | natural abundance | 90 % |
Agilent DD2 - 600 MHz
State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details 50mM phosphate buffer NA; 90% H2O, 10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PHD1 finger of KDM5B | [U-13C; U-15N] | 0.8 mM | |
2 | Phosphate buffer | natural abundance | 50 mM | |
3 | D2O | natural abundance | 10 % | |
4 | H2O | natural abundance | 90 % |
Agilent DD2 - 600 MHz
State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details 50mM phosphate buffer NA; 90% H2O, 10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PHD1 finger of KDM5B | [U-13C; U-15N] | 0.8 mM | |
2 | Phosphate buffer | natural abundance | 50 mM | |
3 | D2O | natural abundance | 10 % | |
4 | H2O | natural abundance | 90 % |
Agilent DD2 - 600 MHz
State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details 50mM phosphate buffer NA; 90% H2O, 10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PHD1 finger of KDM5B | [U-13C; U-15N] | 0.8 mM | |
2 | Phosphate buffer | natural abundance | 50 mM | |
3 | D2O | natural abundance | 10 % | |
4 | H2O | natural abundance | 90 % |
Agilent DD2 - 600 MHz
State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details 50mM phosphate buffer NA; 90% H2O, 10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PHD1 finger of KDM5B | [U-13C; U-15N] | 0.8 mM | |
2 | Phosphate buffer | natural abundance | 50 mM | |
3 | D2O | natural abundance | 10 % | |
4 | H2O | natural abundance | 90 % |
Agilent DD2 - 600 MHz
State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details 50mM phosphate buffer NA; 90% H2O, 10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | PHD1 finger of KDM5B | [U-13C; U-15N] | 0.8 mM | |
2 | Phosphate buffer | natural abundance | 50 mM | |
3 | D2O | natural abundance | 10 % | |
4 | H2O | natural abundance | 90 % |
Agilent DD2 - 600 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details 50mM phosphate buffer NA; 100% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
5 | PHD1 finger of KDM5B | [U-13C; U-15N] | 0.8 mM | |
6 | Phosphate buffer | natural abundance | 50 mM | |
7 | D2O | natural abundance | 100 % |
Agilent DD2 - 600 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details 50mM phosphate buffer NA; 100% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
5 | PHD1 finger of KDM5B | [U-13C; U-15N] | 0.8 mM | |
6 | Phosphate buffer | natural abundance | 50 mM | |
7 | D2O | natural abundance | 100 % |
Agilent DD2 - 600 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details 50mM phosphate buffer NA; 100% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
5 | PHD1 finger of KDM5B | [U-13C; U-15N] | 0.8 mM | |
6 | Phosphate buffer | natural abundance | 50 mM | |
7 | D2O | natural abundance | 100 % |
Agilent DD2 - 600 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details 50mM phosphate buffer NA; 100% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
5 | PHD1 finger of KDM5B | [U-13C; U-15N] | 0.8 mM | |
6 | Phosphate buffer | natural abundance | 50 mM | |
7 | D2O | natural abundance | 100 % |
Agilent DD2 - 600 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details 50mM phosphate buffer NA; 100% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
5 | PHD1 finger of KDM5B | [U-13C; U-15N] | 0.8 mM | |
6 | Phosphate buffer | natural abundance | 50 mM | |
7 | D2O | natural abundance | 100 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_19913_2mny.nef |
Input source #2: Coordindates | 2mny.cif |
Diamagnetism of the molecular assembly | True (excluding Oxygen atoms) |
Whether the assembly has a disulfide bond | None |
Whether the assembly has a other bond | True (see coodinates for details) |
Whether the assembly contains a cyclic polymer | None |
Overall data processing status | Warning |
Disulfide bonds
NoneOther bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
Ptnr_site_1 | Ptnr_site_2 | Redox_state_prediction_1 | Redox_state_prediction_2 | Distance (Å) |
---|---|---|---|---|
1:30:HIS:ND1 | 2:1:ZN:ZN | unknown | unknown | n/a |
1:22:CYS:SG | 2:2:ZN:ZN | unknown | unknown | n/a |
1:48:CYS:SG | 2:2:ZN:ZN | unknown | unknown | n/a |
1:51:CYS:SG | 2:2:ZN:ZN | unknown | unknown | n/a |
1:25:CYS:SG | 2:2:ZN:ZN | unknown | unknown | n/a |
1:7:CYS:SG | 2:1:ZN:ZN | unknown | unknown | n/a |
1:33:CYS:SG | 2:1:ZN:ZN | unknown | unknown | n/a |
1:10:CYS:SG | 2:1:ZN:ZN | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
B | 1 | ZN | ZINC ION | None |
B | 2 | ZN | ZINC ION | None |
Sequence alignments
--310-------320-------330-------340-------350-------360 AVDLYVCLLCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKCLAQE ||||||||||||||||||||||||||||||||||||||||||||||||||||||| AVDLYVCLLCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKCLAQE --------10--------20--------30--------40--------50-----
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 55 | 0 | 0 | 100.0 |
Content subtype: combined_19913_2mny.nef
Assigned chemical shifts
--310-------320-------330-------340-------350-------360 AVDLYVCLLCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKCLAQE ||||||||||||||||||||||||||||||||||| ||||||||||||||||||| AVDLYVCLLCGSGNDEDRLLLCDGCDDSYHTFCLI.PLHDVPKGDWRCPKCLAQE
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 314 | 256 | 81.5 |
13C chemical shifts | 241 | 189 | 78.4 |
15N chemical shifts | 56 | 51 | 91.1 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 110 | 104 | 94.5 |
13C chemical shifts | 110 | 103 | 93.6 |
15N chemical shifts | 51 | 50 | 98.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 204 | 152 | 74.5 |
13C chemical shifts | 131 | 86 | 65.6 |
15N chemical shifts | 5 | 1 | 20.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 29 | 22 | 75.9 |
13C chemical shifts | 29 | 21 | 72.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 23 | 18 | 78.3 |
13C chemical shifts | 22 | 0 | 0.0 |
15N chemical shifts | 1 | 0 | 0.0 |
Covalent bonds
Distance restraints
--310-------320-------330-------340-------350-------360 AVDLYVCLLCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKCLAQE ||||||||||||||||||||||||||||||||||||||||||||||||||||||| AVDLYVCLLCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKCLAQE
Dihedral angle restraints
--310-------320-------330-------340-------350-------360 AVDLYVCLLCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKCLAQE |||| ||||||||| |||||| ||||||||||||||||||||| ....YVCL.....NDEDRLLLC....DSYHTF.LIPPLHDVPKGDWRCPKCLAQ --310-------320-------330-------340-------350---------