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1ik7

Crystal Structure of the Uncomplexed Pelle Death Domain

Method: X-RAY DIFFRACTION Dmax: 98.9 Å Quality: REASONABLE
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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 26–129 Fragment：Death Domain 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 26–129 Fragment：Death Domain 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

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 1IK7 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 ligand/ion 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 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
1YGO Solution Structure of the pelle Death Domain Deposited 2005-01-05 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 26–131（106 aa） Fragment：Pelle Kinase death domain residues 26-131
Not recorded No recorded non-water small molecule 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

2 other PDB entries and 3 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 5–108； UniProt 26–129 Author chain B； PDBConstruct 5–108； UniProt 26–129

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 1ik7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ik7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ik7
Deposition date deposition_date2001-05-02
Structure title titleCrystal Structure of the Uncomplexed Pelle Death Domain
Keywords keywordssiNgle helix, MPD crystallization, structural transition, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.48 Å
Radius of gyration Rg (electron density) rg_electron25.44 Å
Forward intensity I(0) i02820700.00
Molecular weight molecular_weight12576.0 kDa
Excluded volume excluded_volume16014 ų
Envelope volume envelope_volume22316 ų
Hydration-shell volume shell_volume9661 ų
Envelope diameter envelope_diameter102.2 Å
Shell Rg shell_rg25.44 Å
Envelope Rg envelope_rg26.86 Å
Shape Rg shape_rg25.36 Å
Total Rg total_rg25.69 Å
Total atoms total_atoms888
Residues n_residues101
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 dmax98.9 Å
Rg (real space) rg_real25.34 Å
Rg uncertainty (real space) rg_real_error1.30 Å
I(0) (real space) i0_real2.8210e+06
I(0) uncertainty (real space) i0_real_error5.0350e+04
Rg (reciprocal space) rg_reciprocal25.13 Å
I(0) (reciprocal space) i0_reciprocal2820000.0000
Solution quality estimate total_estimate0.6634
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.3 Å
Skewness Skewness skewness0.756
Kurtosis Kurtosis kurtosis-0.013
Angular range angular_range— – 0.3250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha149200.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.209; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.007; Smooth: 0.986
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1ik7a_
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_idd1ik7b_
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

CATH v4.4 (2 domains)

Domain ID domain_id1ik7A00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily530 — Single helix bin
Domain ID domain_id1ik7B00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily530 — Single helix bin
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8. Citations (1)

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9. Files and Curves (10)