2iui

Crystal structure of the PI3-kinase p85 N-terminal SH2 domain in complex with PDGFR phosphotyrosyl peptide

Method: X-RAY DIFFRACTION Dmax: 69.2 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Phosphatidylinositol 3-kinase regulatory subunit alpha

Homo sapiens

UniProt P27986

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 321–440 Fragment:N-TERMINAL SH2 DOMAIN, RESIDUES 321-440 Platelet-derived growth factor receptor beta × 1 (P09619) X-RAY DIFFRACTION X-ray crystallization conditions:0.1M SODIUM ACETATE PH 4.6, 0.2M AMMONIUM ACETATE, 30% PEG4000 Resolution 2.40 Å R-free 0.248
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 321–440 Fragment:N-TERMINAL SH2 DOMAIN, RESIDUES 321-440 Platelet-derived growth factor receptor beta × 1 (P09619) X-RAY DIFFRACTION X-ray crystallization conditions:0.1M SODIUM ACETATE PH 4.6, 0.2M AMMONIUM ACETATE, 30% PEG4000 Resolution 2.40 Å R-free 0.248

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

103 other PDB entries and 115 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name P85A_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–120; UniProt 321–440 Author chain B; PDBConstruct 1–120; UniProt 321–440

Platelet-derived growth factor receptor beta

OrganismNot specified

UniProt P09619

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 748–758 Non-standard monomer:Yes (specific site not provided by mmCIF) Phosphatidylinositol 3-kinase regulatory subunit alpha × 1 (P27986) X-RAY DIFFRACTION X-ray crystallization conditions:0.1M SODIUM ACETATE PH 4.6, 0.2M AMMONIUM ACETATE, 30% PEG4000 Resolution 2.40 Å R-free 0.248
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 748–758 Non-standard monomer:Yes (specific site not provided by mmCIF) Phosphatidylinositol 3-kinase regulatory subunit alpha × 1 (P27986) X-RAY DIFFRACTION X-ray crystallization conditions:0.1M SODIUM ACETATE PH 4.6, 0.2M AMMONIUM ACETATE, 30% PEG4000 Resolution 2.40 Å R-free 0.248

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PGFRB_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–11; UniProt 748–758 Author chain D; PDBConstruct 1–11; UniProt 748–758

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2iui

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2iui
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2iui
Deposition date deposition_date2006-06-03
Structure title titleCrystal structure of the PI3-kinase p85 N-terminal SH2 domain in complex with PDGFR phosphotyrosyl peptide
Keywords keywordsTRANSFERASE, PHOSPHORYLATION, P85, SH2, PI3K, SH2 DOMAIN, SH3 DOMAIN, PI3-KINASE, DISEASE MUTATION; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.46
Radius of gyration Rg (electron density) rg_electron20.49
Forward intensity I(0) i014083400.00
Molecular weight molecular_weight27990.0 kDa
Excluded volume excluded_volume34927 ų
Envelope volume envelope_volume41903 ų
Hydration-shell volume shell_volume17599 ų
Envelope diameter envelope_diameter71.0
Shell Rg shell_rg26.06
Envelope Rg envelope_rg20.57
Shape Rg shape_rg20.43
Total Rg total_rg21.44
Total atoms total_atoms1970
Residues n_residues237
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax69.2
Rg (real space) rg_real21.47
Rg uncertainty (real space) rg_real_error0.44
I(0) (real space) i0_real1.4080e+07
I(0) uncertainty (real space) i0_real_error1.7260e+05
Rg (reciprocal space) rg_reciprocal21.47
I(0) (reciprocal space) i0_reciprocal14080000.0000
Solution quality estimate total_estimate0.8872
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.4
Skewness Skewness skewness0.306
Kurtosis Kurtosis kurtosis-0.576
Angular range angular_range— – 0.3700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4656000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.852; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.999

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2iuia1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.93 — SH2-like
Superfamily Superfamily superfamilyd.93.1 — SH2 domain
Family Family familyd.93.1.1 — SH2 domain
Domain ID domain_idd2iuia2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2iuib1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.93 — SH2-like
Superfamily Superfamily superfamilyd.93.1 — SH2 domain
Family Family familyd.93.1.1 — SH2 domain
Domain ID domain_idd2iuib2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id2iuiA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily10 — SH2 domain
Domain ID domain_id2iuiB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily10 — SH2 domain

8. Citations (1)

9. Files and Curves (10)