SAXSdb — 2zne

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	16-meric peptide from Programmed cell death 6-interacting protein × 1 （Q8WUM4） ZINC ION × 4 SODIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	16-meric peptide from Programmed cell death 6-interacting protein × 1 （Q8WUM4） ZINC ION × 4 SODIUM ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	16-meric peptide from Programmed cell death 6-interacting protein × 2 （Q8WUM4） ZINC ION × 8 SODIUM ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDCD6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–169； UniProt 2–191 Author chain B； PDBConstruct 1–169； UniProt 2–191

16-meric peptide from Programmed cell death 6-interacting protein

OrganismNot specified

UniProt Q8WUM4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Programmed cell death protein 6 × 1 （O75340） ZINC ION × 4 SODIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Programmed cell death protein 6 × 1 （O75340） ZINC ION × 4 SODIUM ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Programmed cell death protein 6 × 2 （O75340） ZINC ION × 8 SODIUM ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDC6I_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–16； UniProt 799–814 Author chain D； PDBConstruct 1–16； UniProt 799–814

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	2zne
Deposition date deposition_date	2008-04-22
Structure title title	Crystal structure of Zn2+-bound form of des3-23ALG-2 complexed with Alix ABS peptide
Keywords keywords	;PENTA-EF-HAND PROTEIN, CALCIUM BINDING PROTEIN, Apoptosis, Endoplasmic reticulum, Membrane, Nucleus, Polymorphism, Cytoplasm, Host-virus interaction, Protein transport, Transport ;; APOPTOSIS
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2zne__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2zne__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zne__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	19.12 Å
Rg (electron density)	18.00 Å
Total Rg	18.95 Å
Atom count	1521
Residues	183
Excluded volume	26851 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zne__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2zne__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2zne__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Programmed cell death protein 6
Molecular weight formula_weight	19877.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3080

ADQSFLWNVFQRVDKDRSGVISDTELQQALSNGTWTPFNPVTVRSIISMFDRENKAGVNFSEFTGVWKYITDWQNVFRTYDRDNSGMIDKNELKQALSGFGYRLSDQFHDILIRKFDRQGRGQIAFDDFIQGCIVLQRLTDIFRRYDTDQDGWIQVSYEQYLSMVFSIV

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	16-meric peptide from Programmed cell death 6-interacting protein
Molecular weight formula_weight	1771.9 kDa
Mutation mutation	C15S
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

QGPPYPTYPGYPGYSQ

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	68

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2zneA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	2zneB00
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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Unit-cell length a length_a	47.449 Å
Unit-cell length b length_b	88.509 Å
Unit-cell length c length_c	211.556 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	33.940 Å
R factor r_factor	0.2255
R_work r_work	0.2228
R_free r_free	0.2739

Crystal structure of Zn2+-bound form of des3-23ALG-2 complexed with Alix ABS peptide

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

16-meric peptide from Programmed cell death 6-interacting protein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2zne__assembly_1__model_1

2zne__assembly_1__model_1 | I(q)

2zne__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Zn2+-bound form of des3-23ALG-2 complexed with Alix ABS peptide

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

16-meric peptide from Programmed cell death 6-interacting protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2zne__assembly_1__model_1

2zne__assembly_1__model_1 | I(q)

2zne__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)