2zrs

Crystal structure of Ca2+-bound form of des3-23ALG-2

Method: X-RAY DIFFRACTION

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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 homooligomer	Homooligomer	Protein 2	CALCIUM ION × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 6	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 6	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 7	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 1–168； UniProt 24–191 Author chain B； PDBConstruct 1–168； UniProt 24–191 Author chain C； PDBConstruct 1–168； UniProt 24–191 Author chain D； PDBConstruct 1–168； UniProt 24–191 Author chain E； PDBConstruct 1–168； UniProt 24–191 Author chain F； PDBConstruct 1–168； UniProt 24–191 Author chain G； PDBConstruct 1–168； UniProt 24–191 Author chain H； PDBConstruct 1–168； UniProt 24–191

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	2zrs
Deposition date deposition_date	2008-09-01
Structure title title	Crystal structure of Ca2+-bound form of des3-23ALG-2
Keywords keywords	Penta-EF-hand protein, Calcium-binding protein, APOPTOSIS, Calcium, Endoplasmic reticulum, Membrane, Nucleus, Polymorphism; 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.

2zrs__assembly_1__model_1

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

Download this curve (.dat)

2zrs__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zrs__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.14 Å
Rg (electron density)	22.86 Å
Total Rg	23.65 Å
Atom count	2745
Residues	328
Excluded volume	48452 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zrs__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2zrs__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2zrs__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2zrs__assembly_4__model_1`	dimeric （2）	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 (2)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2zrsa_
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

Domain ID domain_id	d2zrsb_
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

Domain ID domain_id	d2zrsc_
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

Domain ID domain_id	d2zrsd_
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

Domain ID domain_id	d2zrse_
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

Domain ID domain_id	d2zrsf_
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

Domain ID domain_id	d2zrsg_
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

Domain ID domain_id	d2zrsh_
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 (8 domains)

Domain ID domain_id	2zrsA00
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	2zrsB00
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	2zrsC00
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	2zrsD00
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	2zrsE00
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	2zrsF00
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	2zrsG00
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	2zrsH00
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	54.780 Å
Unit-cell length b length_b	154.425 Å
Unit-cell length c length_c	237.676 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	32

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

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2276
R_work r_work	0.2218
R_free r_free	0.2798

Description description	Programmed cell death protein 6
Molecular weight formula_weight	19806.1 kDa
Source method src_method	man
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	10956

Crystal structure of Ca2+-bound form of des3-23ALG-2

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2zrs__assembly_1__model_1

2zrs__assembly_1__model_1 | I(q)

2zrs__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

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

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	25

Crystal structure of Ca2+-bound form of des3-23ALG-2

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2zrs__assembly_1__model_1

2zrs__assembly_1__model_1 | I(q)

2zrs__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)