Solution structure of the Vav1 SH2 domain complexed with a Syk-derived doubly phosphorylated peptide
GHMQDLSVHL WYAGPMERAG AESILANRSD GTFLVRQRVK DAAEFAISIK YNVEVKHIKI MTAEGLYRIT EKKAFRGLTE LVEFYQQNSL KDCFKSLDTT LQFPFKE
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 79.2 % (1109 of 1401) | 88.2 % (643 of 729) | 67.4 % (370 of 549) | 78.0 % (96 of 123) |
Backbone | 74.3 % (520 of 700) | 92.0 % (219 of 238) | 58.9 % (205 of 348) | 84.2 % (96 of 114) |
Sidechain | 83.9 % (682 of 813) | 86.4 % (424 of 491) | 82.4 % (258 of 313) | 0.0 % (0 of 9) |
Aromatic | 81.0 % (102 of 126) | 82.5 % (52 of 63) | 80.6 % (50 of 62) | 0.0 % (0 of 1) |
Methyl | 90.5 % (114 of 126) | 92.1 % (58 of 63) | 88.9 % (56 of 63) |
1. entity 1
GHMQDLSVHL WYAGPMERAG AESILANRSD GTFLVRQRVK DAAEFAISIK YNVEVKHIKI MTAEGLYRIT EKKAFRGLTE LVEFYQQNSL KDCFKSLDTT LQFPFKE2. entity 2
DTEVXESPXA DPESolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 1.1 mM | |
2 | TRIS | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | DTT | natural abundance | 1 mM | |
5 | sodium azide | natural abundance | 0.02 % | |
6 | entity_2 | natural abundance | 1.1 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 1.1 mM | |
2 | TRIS | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | DTT | natural abundance | 1 mM | |
5 | sodium azide | natural abundance | 0.02 % | |
6 | entity_2 | natural abundance | 1.1 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 1.1 mM | |
2 | TRIS | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | DTT | natural abundance | 1 mM | |
5 | sodium azide | natural abundance | 0.02 % | |
6 | entity_2 | natural abundance | 1.1 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 1.1 mM | |
2 | TRIS | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | DTT | natural abundance | 1 mM | |
5 | sodium azide | natural abundance | 0.02 % | |
6 | entity_2 | natural abundance | 1.1 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 1.1 mM | |
2 | TRIS | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | DTT | natural abundance | 1 mM | |
5 | sodium azide | natural abundance | 0.02 % | |
6 | entity_2 | natural abundance | 1.1 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 1.1 mM | |
2 | TRIS | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | DTT | natural abundance | 1 mM | |
5 | sodium azide | natural abundance | 0.02 % | |
6 | entity_2 | natural abundance | 1.1 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 1.1 mM | |
2 | TRIS | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | DTT | natural abundance | 1 mM | |
5 | sodium azide | natural abundance | 0.02 % | |
6 | entity_2 | natural abundance | 1.1 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 1.1 mM | |
2 | TRIS | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | DTT | natural abundance | 1 mM | |
5 | sodium azide | natural abundance | 0.02 % | |
6 | entity_2 | natural abundance | 1.1 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 1.1 mM | |
2 | TRIS | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | DTT | natural abundance | 1 mM | |
5 | sodium azide | natural abundance | 0.02 % | |
6 | entity_2 | natural abundance | 1.1 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 1.1 mM | |
2 | TRIS | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | DTT | natural abundance | 1 mM | |
5 | sodium azide | natural abundance | 0.02 % | |
6 | entity_2 | natural abundance | 1.1 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 1.1 mM | |
2 | TRIS | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | DTT | natural abundance | 1 mM | |
5 | sodium azide | natural abundance | 0.02 % | |
6 | entity_2 | natural abundance | 1.1 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 1.1 mM | |
2 | TRIS | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | DTT | natural abundance | 1 mM | |
5 | sodium azide | natural abundance | 0.02 % | |
6 | entity_2 | natural abundance | 1.1 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 1.1 mM | |
2 | TRIS | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | DTT | natural abundance | 1 mM | |
5 | sodium azide | natural abundance | 0.02 % | |
6 | entity_2 | natural abundance | 1.1 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 1.1 mM | |
2 | TRIS | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | DTT | natural abundance | 1 mM | |
5 | sodium azide | natural abundance | 0.02 % | |
6 | entity_2 | natural abundance | 1.1 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-13C; U-15N] | 1.1 mM | |
2 | TRIS | natural abundance | 20 mM | |
3 | sodium chloride | natural abundance | 100 mM | |
4 | DTT | natural abundance | 1 mM | |
5 | sodium azide | natural abundance | 0.02 % | |
6 | entity_2 | natural abundance | 1.1 mM | |
7 | H2O | natural abundance | 90 % | |
8 | D2O | natural abundance | 10 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints | combined_17632_2lct.nef |
Input source #2: Coordindates | 2lct.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 (Ã…) |
---|---|---|---|---|
2:4:VAL:C | 2:5:PTR:N | unknown | unknown | n/a |
2:5:PTR:C | 2:6:GLU:N | unknown | unknown | n/a |
2:8:PRO:C | 2:9:PTR:N | unknown | unknown | n/a |
2:9:PTR:C | 2:10:ALA:N | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
B | 342 | PTR | O-PHOSPHOTYROSINE | Assigned chemical shifts, Distance restraints, Coordinates |
B | 346 | PTR | O-PHOSPHOTYROSINE | Assigned chemical shifts, Distance restraints, Coordinates |
Sequence alignments
-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760 GHMQDLSVHLWYAGPMERAGAESILANRSDGTFLVRQRVKDAAEFAISIKYNVEVKHIKIMTAEGLYRITEKKAFRGLTELVEFYQQNSLKDCFKSLDTT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GHMQDLSVHLWYAGPMERAGAESILANRSDGTFLVRQRVKDAAEFAISIKYNVEVKHIKIMTAEGLYRITEKKAFRGLTELVEFYQQNSLKDCFKSLDTT --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 ------- LQFPFKE ||||||| LQFPFKE -------
--340-----350 DTEVXESPXADPE ||||||||||||| DTEVXESPXADPE --------10---
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 107 | 0 | 0 | 100.0 |
B | B | 13 | 0 | 0 | 100.0 |
Content subtype: combined_17632_2lct.nef
Assigned chemical shifts
-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760 GHMQDLSVHLWYAGPMERAGAESILANRSDGTFLVRQRVKDAAEFAISIKYNVEVKHIKIMTAEGLYRITEKKAFRGLTELVEFYQQNSLKDCFKSLDTT ||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| .HMQDLSVHLWYAGPMERAGAESILANRSDGTFLVRQR......FAISIKYNVEVKHIKIMTAEGLYRITEKKAFRGLTELVEFYQQNSLKDCFKSLDTT ------- LQFPFKE ||||||| LQFPFKE
--340-----350 DTEVXESPXADPE ||||||||||||| DTEVXESPXADPE
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 673 | 583 | 86.6 |
13C chemical shifts | 506 | 355 | 70.2 |
15N chemical shifts | 120 | 95 | 79.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 218 | 198 | 90.8 |
13C chemical shifts | 214 | 98 | 45.8 |
15N chemical shifts | 105 | 95 | 90.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 455 | 385 | 84.6 |
13C chemical shifts | 292 | 257 | 88.0 |
15N chemical shifts | 15 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 62 | 55 | 88.7 |
13C chemical shifts | 62 | 55 | 88.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 63 | 51 | 81.0 |
13C chemical shifts | 62 | 49 | 79.0 |
15N chemical shifts | 1 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 72 | 69 | 95.8 |
13C chemical shifts | 57 | 0 | 0.0 |
15N chemical shifts | 11 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 24 | 23 | 95.8 |
13C chemical shifts | 26 | 0 | 0.0 |
15N chemical shifts | 11 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 48 | 46 | 95.8 |
13C chemical shifts | 31 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 4 | 4 | 100.0 |
13C chemical shifts | 4 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 8 | 8 | 100.0 |
13C chemical shifts | 8 | 0 | 0.0 |
Covalent bonds
Distance restraints
-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760 GHMQDLSVHLWYAGPMERAGAESILANRSDGTFLVRQRVKDAAEFAISIKYNVEVKHIKIMTAEGLYRITEKKAFRGLTELVEFYQQNSLKDCFKSLDTT ||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||| .HMQDLSVHLWYAGPMERAGAESILANRSDGTFLVRQR......FAISIKYNVEVKHIKIMTAEGLYRITEKKAFRGLTELVEFYQQNSLKDCFKSLDT. -------670-------680-------690-------700-------710-------720-------730-------740-------750-------760 ------- LQFPFKE |||||| LQFPFK ------
--340-----350 DTEVXESPXADPE ||| ||||| ..EVX.SPXAD --340------