SAXSdb — 3aak

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

Programmed cell death protein 6

Homo sapiens

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–191	Fragment：residues 2-191 Mutation：deletions of residues 3-20, F122A	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% 2-methyl-2,4-pentanediol, 100mM Cacodylate, 50mM Zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.298

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 3AAK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2ZN8 Crystal structure of Zn2+-bound form of ALG-2 Deposited 2008-04-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–191（190 aa）	Not recorded	ZN ZINC ION × 8 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% 2-methyl-2,4-pentanediol, 100mM Cacodylate, 75mM Zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.260
2ZN9 Crystal structure of Ca2+-bound form of des3-20ALG-2 Deposited 2008-04-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–191（172 aa） Fragment：residues 20-191 Chain B 20–191（172 aa） Fragment：residues 20-191	Not recorded	CA CALCIUM ION × 7 2PE NONAETHYLENE GLYCOL × 1 12P DODECAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；18% PEG 8000, 0.1M Sodium Cacodylate, 0.2M Calcium Acetate hydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.40 Å R-free 0.298
2ZN9 Crystal structure of Ca2+-bound form of des3-20ALG-2 Deposited 2008-04-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–191（172 aa） Fragment：residues 20-191 Chain B 20–191（172 aa） Fragment：residues 20-191	Not recorded	CA CALCIUM ION × 7 2PE NONAETHYLENE GLYCOL × 1 12P DODECAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；18% PEG 8000, 0.1M Sodium Cacodylate, 0.2M Calcium Acetate hydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.40 Å R-free 0.298
2ZND Crystal structure of Ca2+-free form of des3-20ALG-2 Deposited 2008-04-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–191（172 aa） Fragment：residues 20-191	Not recorded	MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 10 PO4 PHOSPHATE ION × 4 NA SODIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；40% 2-methyl-2,4-pentanediol, 0.1M Na2HPO4-KH2PO4, 2mM EDTA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.222
2ZNE Crystal structure of Zn2+-bound form of des3-23ALG-2 complexed with Alix ABS peptide Deposited 2008-04-22	Different mutation/modification 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 2–191（190 aa） Fragment：residues 2-191	Not recorded	ZN ZINC ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% 2-propanol, 0.1M Cacodylate, 0.2M zinc acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274
2ZNE Crystal structure of Zn2+-bound form of des3-23ALG-2 complexed with Alix ABS peptide Deposited 2008-04-22	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–191（190 aa） Fragment：residues 2-191	Not recorded	ZN ZINC ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% 2-propanol, 0.1M Cacodylate, 0.2M zinc acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274
2ZNE Crystal structure of Zn2+-bound form of des3-23ALG-2 complexed with Alix ABS peptide Deposited 2008-04-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–191（190 aa） Fragment：residues 2-191 Chain B 2–191（190 aa） Fragment：residues 2-191	Not recorded	ZN ZINC ION × 8 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% 2-propanol, 0.1M Cacodylate, 0.2M zinc acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274
2ZRS Crystal structure of Ca2+-bound form of des3-23ALG-2 Deposited 2008-09-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 24–191（168 aa） Fragment：UNP residues 24-191 Chain B 24–191（168 aa） Fragment：UNP residues 24-191	Not recorded	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50mM MES, 12.5% 2-propanol, 150mM calcium acetate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.10 Å R-free 0.280
2ZRS Crystal structure of Ca2+-bound form of des3-23ALG-2 Deposited 2008-09-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 24–191（168 aa） Fragment：UNP residues 24-191 Chain D 24–191（168 aa） Fragment：UNP residues 24-191	Not recorded	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50mM MES, 12.5% 2-propanol, 150mM calcium acetate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.10 Å R-free 0.280
2ZRS Crystal structure of Ca2+-bound form of des3-23ALG-2 Deposited 2008-09-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 24–191（168 aa） Fragment：UNP residues 24-191 Chain F 24–191（168 aa） Fragment：UNP residues 24-191	Not recorded	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50mM MES, 12.5% 2-propanol, 150mM calcium acetate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.10 Å R-free 0.280
2ZRS Crystal structure of Ca2+-bound form of des3-23ALG-2 Deposited 2008-09-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 24–191（168 aa） Fragment：UNP residues 24-191 Chain H 24–191（168 aa） Fragment：UNP residues 24-191	Not recorded	CA CALCIUM ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50mM MES, 12.5% 2-propanol, 150mM calcium acetate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.10 Å R-free 0.280
2ZRT Crystal structure of Zn2+-bound form of des3-23ALG-2 Deposited 2008-09-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 24–191（168 aa） Fragment：UNP residues 24-191 Chain B 24–191（168 aa） Fragment：UNP residues 24-191	Not recorded	ZN ZINC ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100mM MES, 15% ethanol, 200mM zinc acetate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.221
2ZRT Crystal structure of Zn2+-bound form of des3-23ALG-2 Deposited 2008-09-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 24–191（168 aa） Fragment：UNP residues 24-191 Chain D 24–191（168 aa） Fragment：UNP residues 24-191	Not recorded	ZN ZINC ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100mM MES, 15% ethanol, 200mM zinc acetate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.221
2ZRT Crystal structure of Zn2+-bound form of des3-23ALG-2 Deposited 2008-09-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 24–191（168 aa） Fragment：UNP residues 24-191 Chain F 24–191（168 aa） Fragment：UNP residues 24-191	Not recorded	ZN ZINC ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100mM MES, 15% ethanol, 200mM zinc acetate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.221
2ZRT Crystal structure of Zn2+-bound form of des3-23ALG-2 Deposited 2008-09-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 24–191（168 aa） Fragment：UNP residues 24-191 Chain H 24–191（168 aa） Fragment：UNP residues 24-191	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100mM MES, 15% ethanol, 200mM zinc acetate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.221
3AAJ Crystal structure of Ca2+-bound form of des3-23ALG-2deltaGF122 Deposited 2009-11-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–191（190 aa） Fragment：residues 2-191 Chain B 2–191（190 aa） Fragment：residues 2-191	Mutation：deletions of residues 3-23, G121, F122 Mutation：deletions of residues 3-23, G121, F122	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.05M Cacodylate, 2.5% PEG 4000, 0.3M Ammonium acetate, 0.01M CaCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.266
3WXA X-ray crystal structural analysis of the complex between ALG-2 and Sec31A peptide Deposited 2014-07-29	Different construct Different mutation/modification 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 20–191（172 aa） Fragment：UNP residues 20-191	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M Cacodylate, 20% MPD, 0.05M Zinc Acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.36 Å R-free 0.263
3WXA X-ray crystal structural analysis of the complex between ALG-2 and Sec31A peptide Deposited 2014-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–191（172 aa） Fragment：UNP residues 20-191	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M Cacodylate, 20% MPD, 0.05M Zinc Acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.36 Å R-free 0.263
5GQQ Structure of ALG-2/HEBP2 Complex Deposited 2016-08-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 24–191（168 aa） Fragment：UNP RESIDUES 24-191 Chain D 24–191（168 aa） Fragment：UNP RESIDUES 24-191	Not recorded	CA CALCIUM ION × 6 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1 M Bis-Tris, 2 M NaCl, pH 5.5	Resolution 2.20 Å R-free 0.225

9 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PDCD6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–172； UniProt 2–191

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	3aak
Deposition date deposition_date	2009-11-19
Structure title title	Crystal structure of Zn2+-bound form of des3-20ALG-2F122A
Keywords keywords	PENTA-EF-HAND PROTEIN, CALCIUM-BINDING PROTEIN, Apoptosis, Endoplasmic reticulum; 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	19.57 Å
Radius of gyration Rg (electron density) rg_electron	18.43 Å
Forward intensity I(0) i0	7631490.00
Molecular weight molecular_weight	19771.0 kDa
Excluded volume excluded_volume	24473 Å³
Envelope volume envelope_volume	30587 Å³
Hydration-shell volume shell_volume	14659 Å³
Envelope diameter envelope_diameter	65.2 Å
Shell Rg shell_rg	23.52 Å
Envelope Rg envelope_rg	18.64 Å
Shape Rg shape_rg	18.41 Å
Total Rg total_rg	19.33 Å
Total atoms total_atoms	1388
Residues n_residues	167
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	64.5 Å
Rg (real space) rg_real	19.55 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	7.6310e+06
I(0) uncertainty (real space) i0_real_error	1.0170e+05
Rg (reciprocal space) rg_reciprocal	19.55 Å
I(0) (reciprocal space) i0_reciprocal	7632000.0000
Solution quality estimate total_estimate	0.8190
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.9 Å
Skewness Skewness skewness	0.250
Kurtosis Kurtosis kurtosis	-0.447
Angular range angular_range	— – 0.4050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	663100.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Programmed cell death protein 6
Molecular weight formula_weight	20082.4 kDa
Mutation mutation	deletions of residues 3-20, F122A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1404

AALPDQSFLWNVFQRVDKDRSGVISDTELQQALSNGTWTPFNPVTVRSIISMFDRENKAGVNFSEFTGVWKYITDWQNVFRTYDRDNSGMIDKNELKQALSGAGYRLSDQFHDILIRKFDRQGRGQIAFDDFIQGCIVLQRLTDIFRRYDTDQDGWIQVSYEQYLSMVFSIV

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	16

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3aaka_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	3aakA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

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8. Citations (1)

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Unit-cell length a length_a	71.266 Å
Unit-cell length b length_b	170.209 Å
Unit-cell length c length_c	46.911 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	32.240 Å
R factor r_factor	0.2542
R_work r_work	0.2521
R_free r_free	0.2983

fit	/app/data/saxs_computation/aa/3aak/3aak.fit
pddf	/app/data/pr_computation/aa/3aak/3aak.pr.out
profile	/app/data/saxs_computation/aa/3aak/3aak.dat

Crystal structure of Zn2+-bound form of des3-20ALG-2F122A

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

Programmed cell death protein 6

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