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Biological Magnetic Resonance Data Bank


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BMRB Entry 19423

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19423
MolProbity Validation Chart

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Title: Solution structure of the Vav1 SH2 domain complexed with a Syk-derived singly phosphorylated peptide   PubMed: 23955592

Deposition date: 2013-08-13 Original release date: 2013-08-26

Authors: Chen, Chih-Hong; Piraner, Dan; Gorenstein, Nina; Geahlen, Robert; Post, Carol

Citation: Chen, Chih-Hong; Piraner, Dan; Gorenstein, Nina; Geahlen, Robert; Beth Post, Carol. "Differential recognition of syk-binding sites by each of the two phosphotyrosine-binding pockets of the Vav SH2 domain."  Biopolymers 99, 897-907 (2013).

Assembly members:
entity_1, polymer, 106 residues, 12335.253 Da.
entity_2, polymer, 13 residues, 1594.495 Da.
O-PHOSPHOTYROSINE, non-polymer, 261.168 Da.

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
entity_1: HMQDLSVHLWYAGPMERAGA ESILANRSDGTFLVRQRVKD AAEFAISIKYNVEVKHIKIM TAEGLYRITEKKAFRGLTEL VEFYQQNSLKDCFKSLDTTL QFPFKE
entity_2: DTEVYESPXADPE

Data sets:
Data typeCount
13C chemical shifts315
15N chemical shifts92
1H chemical shifts681

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1Vav1 SH2 domain binding pocket_11
2Vav1 SH2 domain binding pocket_22
3entity_PTR3

Entities:

Entity 1, Vav1 SH2 domain binding pocket_1 106 residues - 12335.253 Da.

1   HISMETGLNASPLEUSERVALHISLEUTRP
2   TYRALAGLYPROMETGLUARGALAGLYALA
3   GLUSERILELEUALAASNARGSERASPGLY
4   THRPHELEUVALARGGLNARGVALLYSASP
5   ALAALAGLUPHEALAILESERILELYSTYR
6   ASNVALGLUVALLYSHISILELYSILEMET
7   THRALAGLUGLYLEUTYRARGILETHRGLU
8   LYSLYSALAPHEARGGLYLEUTHRGLULEU
9   VALGLUPHETYRGLNGLNASNSERLEULYS
10   ASPCYSPHELYSSERLEUASPTHRTHRLEU
11   GLNPHEPROPHELYSGLU

Entity 2, Vav1 SH2 domain binding pocket_2 13 residues - 1594.495 Da.

1   ASPTHRGLUVALTYRGLUSERPROPTRALA
2   ASPPROGLU

Entity 3, entity_PTR - C9 H12 N O6 P - 261.168 Da.

1   PTR

Samples:

sample_1: entity_1, [U-99% 13C; U-99% 15N], 1 mM; entity_2 1 mM; TRIS 20 mM; sodium chloride 100 mM; DTT 1 mM; sodium azide 0.02%; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 120 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

CYANA, Guntert, Mumenthaler and Wuthrich - chemical shift assignment, structure solution

NMR spectrometers:

  • Bruker Avance 800 MHz

Related Database Links:

BMRB 17632
PDB
DBJ BAG36112 BAG62721 BAJ21026
EMBL CAA34383 CAA58783
GB AAC25011 AAH13361 AAI23647 AIC59346 EAW69057
REF NP_001071542 NP_001245135 NP_001245136 NP_001254762 NP_005419
SP P15498 Q08DN7
TPG DAA27902

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts