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1ygo

Solution Structure of the pelle Death Domain

Method: SOLUTION NMR Dmax: 57.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Probable serine/threonine-protein kinase pelle

Drosophila melanogaster

UniProt Q05652

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 26–131 Fragment：Pelle Kinase death domain residues 26-131 No other associated polymer SOLUTION NMR NMR measurement conditions：298 K NMR sample composition：1mM Pelle death domain, U-15N, 13C; 20mM phosphate, 100mM NaCl, pH 7.6; 10% D20 Resolution not provided

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.

Other PDB Difference from Current Entry 1YGO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D2Z THREE-DIMENSIONAL STRUCTURE OF A COMPLEX BETWEEN THE DEATH DOMAINS OF PELLE AND TUBE Deposited 1999-09-28 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 26–129（104 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；20-25% PEG 2000 monomethyl ether, 100 mM Hepes pH 7.2-8.4 0-200 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.00 Å R-free 0.244
1D2Z THREE-DIMENSIONAL STRUCTURE OF A COMPLEX BETWEEN THE DEATH DOMAINS OF PELLE AND TUBE Deposited 1999-09-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 26–129（104 aa）
Not recorded EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；20-25% PEG 2000 monomethyl ether, 100 mM Hepes pH 7.2-8.4 0-200 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.00 Å R-free 0.244
1IK7 Crystal Structure of the Uncomplexed Pelle Death Domain Deposited 2001-05-02 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–129（104 aa） Fragment：Death Domain
Not recorded TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；45% 2-methyl-2,4-pentanediol, Tris, 0.4 M sodium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.30 Å R-free 0.258
1IK7 Crystal Structure of the Uncomplexed Pelle Death Domain Deposited 2001-05-02 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 26–129（104 aa） Fragment：Death Domain
Not recorded TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；45% 2-methyl-2,4-pentanediol, Tris, 0.4 M sodium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.30 Å R-free 0.258

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KPEL_DROME
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–110； UniProt 26–131

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 1ygo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ygo
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ygo
Deposition date deposition_date2005-01-05
Structure title titleSolution Structure of the pelle Death Domain
Keywords keywordsanti-parallel 6 helix bundle, TRANSFERASE; TRANSFERASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.55 Å
Radius of gyration Rg (electron density) rg_electron14.84 Å
Forward intensity I(0) i0876677000.00
Molecular weight molecular_weight253710.0 kDa
Excluded volume excluded_volume319090 ų
Envelope volume envelope_volume39037 ų
Hydration-shell volume shell_volume17851 ų
Envelope diameter envelope_diameter63.3 Å
Shell Rg shell_rg24.71 Å
Envelope Rg envelope_rg19.36 Å
Shape Rg shape_rg14.82 Å
Total Rg total_rg15.11 Å
Total atoms total_atoms36100
Residues n_residues2200
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax57.5 Å
Rg (real space) rg_real15.57 Å
Rg uncertainty (real space) rg_real_error0.43 Å
I(0) (real space) i0_real8.7670e+08
I(0) uncertainty (real space) i0_real_error1.0530e+07
Rg (reciprocal space) rg_reciprocal15.57 Å
I(0) (reciprocal space) i0_reciprocal876700000.0000
Solution quality estimate total_estimate0.7990
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.7 Å
Skewness Skewness skewness0.418
Kurtosis Kurtosis kurtosis-0.027
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha419100.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.511; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.853; Smooth: 0.998
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1ygoa2
Class classa — All alpha proteins
Fold Fold folda.77 — DEATH domain
Superfamily Superfamily superfamilya.77.1 — DEATH domain
Family Family familya.77.1.2 — DEATH domain, DD
Domain ID domain_idd1ygoa3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id1ygoA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology533 — Death Domain, Fas
Homologous superfamily homologous superfamily10 — Death Domain, Fas
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8. Citations (1)

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9. Files and Curves (10)