SAXSdb — 1d2z

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

DEATH DOMAIN OF PELLE

Drosophila melanogaster

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 26–129	Not recorded	DEATH DOMAIN OF TUBE × 1 （P22812）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 26–129	Not recorded	DEATH DOMAIN OF TUBE × 1 （P22812） 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

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 1D2Z	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1IK7 Crystal Structure of the Uncomplexed Pelle Death Domain Deposited 2001-05-02	Different construct Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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
1YGO Solution Structure of the pelle Death Domain Deposited 2005-01-05	Different construct Different oligomeric state 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 1–108； UniProt 26–129 Author chain C； PDBConstruct 1–108； UniProt 26–129

DEATH DOMAIN OF TUBE

Drosophila melanogaster

UniProt P22812

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 B； UniProt 23–175	Not recorded	DEATH DOMAIN OF PELLE × 1 （Q05652）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 23–175	Not recorded	DEATH DOMAIN OF PELLE × 1 （Q05652） 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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	TUBE_DROME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–153； UniProt 23–175 Author chain D； PDBConstruct 1–153； UniProt 23–175

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1d2z
Deposition date deposition_date	1999-09-28
Structure title title	THREE-DIMENSIONAL STRUCTURE OF A COMPLEX BETWEEN THE DEATH DOMAINS OF PELLE AND TUBE
Keywords keywords	SIX-HELIX BUNDLE, LINEAR ARRAY OF DEATH DOMAINS, PLASTIC INTERFACES, APOPTOSIS; APOPTOSIS
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	32.01 Å
Radius of gyration Rg (electron density) rg_electron	32.18 Å
Forward intensity I(0) i0	53806300.00
Molecular weight molecular_weight	58201.0 kDa
Excluded volume excluded_volume	73131 Å³
Envelope volume envelope_volume	96648 Å³
Hydration-shell volume shell_volume	27612 Å³
Envelope diameter envelope_diameter	115.1 Å
Shell Rg shell_rg	35.45 Å
Envelope Rg envelope_rg	32.09 Å
Shape Rg shape_rg	32.17 Å
Total Rg total_rg	32.53 Å
Total atoms total_atoms	4090
Residues n_residues	513
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	108.8 Å
Rg (real space) rg_real	32.44 Å
Rg uncertainty (real space) rg_real_error	0.98 Å
I(0) (real space) i0_real	5.3810e+07
I(0) uncertainty (real space) i0_real_error	8.3670e+05
Rg (reciprocal space) rg_reciprocal	32.26 Å
I(0) (reciprocal space) i0_reciprocal	53800000.0000
Solution quality estimate total_estimate	0.6189
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	26.6 Å
Skewness Skewness skewness	0.541
Kurtosis Kurtosis kurtosis	-0.462
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13820000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.677; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.607; Smooth: 0.676

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DEATH DOMAIN OF PELLE
Molecular weight formula_weight	12446.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4386

GSHMSHLDNTMAIRLLPLPVRAQLCAHLDALDVWQQLATAVKLYPDQVEQISSQKQRGRSASNEFLNIWGGQYNHTVQTLFALFKKLKLHNAMRLIKDYVSEDLHKYI

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	fruit fly
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DEATH DOMAIN OF TUBE
Molecular weight formula_weight	17084.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

LSSKYSRNTELRRVEDNDIYRLAKILDENSCWRKLMSIIPKGMDVQACSGAGCLNFPAEIKKGFKYTAQDVFQIDEAANRLPPDQSKSQMMIDEWKTSGKLNERPTVGVLLQLLVQAELFSAADFVALDFLNESTPARPVDGPGALISLELLE

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	fruit fly
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	266

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1d2za_
Class class	a — All alpha proteins
Fold Fold fold	a.77 — DEATH domain
Superfamily Superfamily superfamily	a.77.1 — DEATH domain
Family Family family	a.77.1.2 — DEATH domain, DD

Domain ID domain_id	d1d2zb_
Class class	a — All alpha proteins
Fold Fold fold	a.77 — DEATH domain
Superfamily Superfamily superfamily	a.77.1 — DEATH domain
Family Family family	a.77.1.2 — DEATH domain, DD

Domain ID domain_id	d1d2zc1
Class class	a — All alpha proteins
Fold Fold fold	a.77 — DEATH domain
Superfamily Superfamily superfamily	a.77.1 — DEATH domain
Family Family family	a.77.1.2 — DEATH domain, DD

Domain ID domain_id	d1d2zc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1d2zd_
Class class	a — All alpha proteins
Fold Fold fold	a.77 — DEATH domain
Superfamily Superfamily superfamily	a.77.1 — DEATH domain
Family Family family	a.77.1.2 — DEATH domain, DD

CATH v4.4 (4 domains)

Domain ID domain_id	1d2zA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

Domain ID domain_id	1d2zB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

Domain ID domain_id	1d2zC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

Domain ID domain_id	1d2zD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

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8. Citations (1)

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Unit-cell length a length_a	58.123 Å
Unit-cell length b length_b	87.495 Å
Unit-cell length c length_c	117.662 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2200
R_work r_work	0.2110
R_free r_free	0.2440

fit	/app/data/saxs_computation/d2/1d2z/1d2z.fit
pddf	/app/data/pr_computation/d2/1d2z/1d2z.pr.out
profile	/app/data/saxs_computation/d2/1d2z/1d2z.dat

THREE-DIMENSIONAL STRUCTURE OF A COMPLEX BETWEEN THE DEATH DOMAINS OF PELLE AND TUBE

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

DEATH DOMAIN OF PELLE

State in the Current Structure

Other States of the Same Protein in the Database

DEATH DOMAIN OF TUBE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)