solution structure of the atypical PDZ-like domain of synbindin
MGHHHHHHLD SYAPRAEAEK TFSYPLDLLL KLHDERVLVA FGQRDGIRVG HAVLAINGMD VNGRYTADGK EVLEYLGNPA NYPVSIRFGR PRLTSN
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 76.4 % (841 of 1101) | 75.3 % (429 of 570) | 76.7 % (333 of 434) | 81.4 % (79 of 97) |
Backbone | 81.8 % (463 of 566) | 81.1 % (159 of 196) | 82.8 % (231 of 279) | 80.2 % (73 of 91) |
Sidechain | 73.0 % (454 of 622) | 72.2 % (270 of 374) | 73.6 % (178 of 242) | 100.0 % (6 of 6) |
Aromatic | 62.7 % (64 of 102) | 64.7 % (33 of 51) | 60.8 % (31 of 51) | |
Methyl | 75.5 % (80 of 106) | 73.6 % (39 of 53) | 77.4 % (41 of 53) |
1. apd
MGHHHHHHLD SYAPRAEAEK TFSYPLDLLL KLHDERVLVA FGQRDGIRVG HAVLAINGMD VNGRYTADGK EVLEYLGNPA NYPVSIRFGR PRLTSNSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | apd | [U-13C; U-15N] | 1.0 ~ 1.5 (±0.1) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | DSS | natural abundance | 0.01 % | |
4 | sodium azide | natural abundance | 0.01 % |
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 - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | apd | [U-13C; U-15N] | 1.0 ~ 1.5 (±0.1) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | DSS | natural abundance | 0.01 % | |
4 | sodium azide | natural abundance | 0.01 % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | apd | [U-13C; U-15N] | 1.0 ~ 1.5 (±0.1) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | DSS | natural abundance | 0.01 % | |
4 | sodium azide | natural abundance | 0.01 % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | apd | [U-13C; U-15N] | 1.0 ~ 1.5 (±0.1) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | DSS | natural abundance | 0.01 % | |
4 | sodium azide | natural abundance | 0.01 % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | apd | [U-13C; U-15N] | 1.0 ~ 1.5 (±0.1) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | DSS | natural abundance | 0.01 % | |
4 | sodium azide | natural abundance | 0.01 % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | apd | [U-13C; U-15N] | 1.0 ~ 1.5 (±0.1) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | DSS | natural abundance | 0.01 % | |
4 | sodium azide | natural abundance | 0.01 % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | apd | [U-13C; U-15N] | 1.0 ~ 1.5 (±0.1) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | DSS | natural abundance | 0.01 % | |
4 | sodium azide | natural abundance | 0.01 % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | apd | [U-13C; U-15N] | 1.0 ~ 1.5 (±0.1) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | DSS | natural abundance | 0.01 % | |
4 | sodium azide | natural abundance | 0.01 % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | apd | [U-13C; U-15N] | 1.0 ~ 1.5 (±0.1) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | DSS | natural abundance | 0.01 % | |
4 | sodium azide | natural abundance | 0.01 % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | apd | [U-13C; U-15N] | 1.0 ~ 1.5 (±0.1) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | DSS | natural abundance | 0.01 % | |
4 | sodium azide | natural abundance | 0.01 % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | apd | [U-13C; U-15N] | 1.0 ~ 1.5 (±0.1) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | DSS | natural abundance | 0.01 % | |
4 | sodium azide | natural abundance | 0.01 % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | apd | [U-13C; U-15N] | 1.0 ~ 1.5 (±0.1) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | DSS | natural abundance | 0.01 % | |
4 | sodium azide | natural abundance | 0.01 % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | apd | [U-13C; U-15N] | 1.0 ~ 1.5 (±0.1) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | DSS | natural abundance | 0.01 % | |
4 | sodium azide | natural abundance | 0.01 % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | apd | [U-13C; U-15N] | 1.0 ~ 1.5 (±0.1) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | DSS | natural abundance | 0.01 % | |
4 | sodium azide | natural abundance | 0.01 % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | apd | [U-13C; U-15N] | 1.0 ~ 1.5 (±0.1) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | DSS | natural abundance | 0.01 % | |
4 | sodium azide | natural abundance | 0.01 % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | apd | [U-13C; U-15N] | 1.0 ~ 1.5 (±0.1) mM | |
2 | potassium phosphate | natural abundance | 50 (±1.0) mM | |
3 | DSS | natural abundance | 0.01 % | |
4 | sodium azide | natural abundance | 0.01 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_15370_2jsn.nef |
Input source #2: Coordindates | 2jsn.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 | None |
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)
NoneNon-standard residues
NoneSequence alignments
--------10--------20--------30--------40--------50--------60--------70--------80--------90------ MGHHHHHHLDSYAPRAEAEKTFSYPLDLLLKLHDERVLVAFGQRDGIRVGHAVLAINGMDVNGRYTADGKEVLEYLGNPANYPVSIRFGRPRLTSN |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MGHHHHHHLDSYAPRAEAEKTFSYPLDLLLKLHDERVLVAFGQRDGIRVGHAVLAINGMDVNGRYTADGKEVLEYLGNPANYPVSIRFGRPRLTSN
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 96 | 0 | 0 | 100.0 |
Content subtype: combined_15370_2jsn.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80--------90------ MGHHHHHHLDSYAPRAEAEKTFSYPLDLLLKLHDERVLVAFGQRDGIRVGHAVLAINGMDVNGRYTADGKEVLEYLGNPANYPVSIRFGRPRLTSN || |||||||||||| |||||| ||||||||||||||| |||||||||||||||||||||||||||||||||||||| ||||||||| .GH..HHHLDSYAPRAE..KTFSYP...LLKLHDERVLVAFGQ.....VGHAVLAINGMDVNGRYTADGKEVLEYLGNPANYPVSI.FGRPRLTSN
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 570 | 425 | 74.6 |
13C chemical shifts | 434 | 328 | 75.6 |
15N chemical shifts | 105 | 76 | 72.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 196 | 157 | 80.1 |
13C chemical shifts | 192 | 150 | 78.1 |
15N chemical shifts | 91 | 69 | 75.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 374 | 268 | 71.7 |
13C chemical shifts | 242 | 178 | 73.6 |
15N chemical shifts | 14 | 7 | 50.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 55 | 40 | 72.7 |
13C chemical shifts | 55 | 42 | 76.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 51 | 31 | 60.8 |
13C chemical shifts | 51 | 31 | 60.8 |
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90------ MGHHHHHHLDSYAPRAEAEKTFSYPLDLLLKLHDERVLVAFGQRDGIRVGHAVLAINGMDVNGRYTADGKEVLEYLGNPANYPVSIRFGRPRLTSN || |||||||||||| |||||| ||||||||||||||| |||||||||||||||||||||||||||||||||||||| ||||||||| .GH..HHHLDSYAPRAE..KTFSYP...LLKLHDERVLVAFGQ.....VGHAVLAINGMDVNGRYTADGKEVLEYLGNPANYPVSI.FGRPRLTSN
--------10--------20--------30--------40--------50--------60--------70--------80--------90------ MGHHHHHHLDSYAPRAEAEKTFSYPLDLLLKLHDERVLVAFGQRDGIRVGHAVLAINGMDVNGRYTADGKEVLEYLGNPANYPVSIRFGRPRLTSN || |||||||||||| |||||| ||||||||||||||| |||||||||||||||||||||||||||||||||||||| ||||||||| .GH..HHHLDSYAPRAE..KTFSYP...LLKLHDERVLVAFGQ.....VGHAVLAINGMDVNGRYTADGKEVLEYLGNPANYPVSI.FGRPRLTSN
Dihedral angle restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90------ MGHHHHHHLDSYAPRAEAEKTFSYPLDLLLKLHDERVLVAFGQRDGIRVGHAVLAINGMDVNGRYTADGKEVLEYLGNPANYPVSIRFGRPRLTSN || |||||| ||||||| ||| |||||||||||| ||||| |||||||| ||| ||||||||| MG.................KTFSYP...LLKLHDE.VLV.........VGHAVLAINGMD...RYTAD.KEVLEYLG.PAN.PVSIRFGRP --------10--------20--------30--------40--------50--------60--------70--------80--------90-
--------10--------20--------30--------40--------50--------60--------70--------80--------90------ MGHHHHHHLDSYAPRAEAEKTFSYPLDLLLKLHDERVLVAFGQRDGIRVGHAVLAINGMDVNGRYTADGKEVLEYLGNPANYPVSIRFGRPRLTSN || |||||| ||||||| ||| |||||||||||| ||||| |||||||| ||| ||||||||| MG.................KTFSYP...LLKLHDE.VLV.........VGHAVLAINGMD...RYTAD.KEVLEYLG.PAN.PVSIRFGRP --------10--------20--------30--------40--------50--------60--------70--------80--------90-