3ll8

Crystal Structure of Calcineurin in Complex with AKAP79 Peptide

Method: X-RAY DIFFRACTION

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

AKAP79 peptide

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform × 1 （Q08209） Calcineurin subunit B type 1 × 1 （P63098） PHOSPHATE ION × 1 ZINC ION × 1 FE (III) ION × 1 CALCIUM ION × 4 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform × 2 （Q08209） Calcineurin subunit B type 1 × 2 （P63098） PHOSPHATE ION × 2 ZINC ION × 2 FE (III) ION × 2 CALCIUM ION × 8 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AKAP5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain E； PDBConstruct 1–11； UniProt 336–346

Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform

Homo sapiens

UniProt Q08209

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	AKAP79 peptide × 1 （P24588） Calcineurin subunit B type 1 × 1 （P63098） PHOSPHATE ION × 1 ZINC ION × 1 FE (III) ION × 1 CALCIUM ION × 4 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Calcineurin subunit B type 1 × 1 （P63098） PHOSPHATE ION × 1 ZINC ION × 1 FE (III) ION × 1 CALCIUM ION × 4 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	AKAP79 peptide × 1 （P24588） Calcineurin subunit B type 1 × 2 （P63098） PHOSPHATE ION × 2 ZINC ION × 2 FE (III) ION × 2 CALCIUM ION × 8 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PP2BA_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–357； UniProt 14–370 Author chain C； PDBConstruct 1–357； UniProt 14–370

Calcineurin subunit B type 1

Homo sapiens

UniProt P63098

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	AKAP79 peptide × 1 （P24588） Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform × 1 （Q08209） PHOSPHATE ION × 1 ZINC ION × 1 FE (III) ION × 1 CALCIUM ION × 4 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform × 1 （Q08209） PHOSPHATE ION × 1 ZINC ION × 1 FE (III) ION × 1 CALCIUM ION × 4 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	AKAP79 peptide × 1 （P24588） Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform × 2 （Q08209） PHOSPHATE ION × 2 ZINC ION × 2 FE (III) ION × 2 CALCIUM ION × 8 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CANB1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 1–155； UniProt 16–170 Author chain D； PDBConstruct 1–155； UniProt 16–170

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	3ll8
Deposition date deposition_date	2010-01-28
Structure title title	Crystal Structure of Calcineurin in Complex with AKAP79 Peptide
Keywords keywords	;protein-peptide docking, protein targeting, calcineurin, AKAP79, beta-augmentation, Calmodulin-binding, Membrane, Hydrolase, Iron, Metal-binding, Nucleus, Phosphoprotein, Protein phosphatase, Lipoprotein, Myristate, Hydrolase-calcium binding protein complex ;; Hydrolase/calcium binding protein
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.

3ll8__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3ll8__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ll8__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	33.62 Å
Rg (electron density)	33.03 Å
Total Rg	33.65 Å
Atom count	8385
Residues	1035
Excluded volume	149900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ll8__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ll8__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3ll8__assembly_3__model_1`	pentameric （5）	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 (8)

Entity 1 Entity 1 polymer

Description description	AKAP79 peptide
Molecular weight formula_weight	1214.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E
Atom count atom_count	8968

EPIAIIITDTE

Entity 2 Entity 2 polymer

Description description	Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
Molecular weight formula_weight	41259.2 kDa
EC 编号 ec_number	3.1.3.16
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

TDRVVKAVPFPPSHRLTAKEVFDNDGKPRVDILKAHLMKEGRLEESVALRIITEGASILRQEKNLLDIDAPVTVCGDIHGQFFDLMKLFEVGGSPANTRYLFLGDYVDRGYFSIECVLYLWALKILYPKTLFLLRGNHECRHLTEYFTFKQECKIKYSERVYDACMDAFDCLPLAALMNQQFLCVHGGLSPEINTLDDIRKLDRFKEPPAYGPMCDILWSDPLEDFGNEKTQEHFTHNTVRGCSYFYSYPAVCEFLQHNNLLSILRAHEAQDAGYRMYRKSQTTGFPSLITIFSAPNYLDVYNNKAAVLKYENNVMNIRQFNCSPHPYWLPNFMDVFTWSLPFVGEKVTEMLVNVLN

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 3 Entity 3 polymer

Description description	Calcineurin subunit B type 1
Molecular weight formula_weight	17624.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

DADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEVDFKEFIEGVSQFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDKTIINADKDGDGRISFEEFCAVVGGLDIHKKMVVDV

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 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	583

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3ll8A00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Metallo-dependent phosphatases

Domain ID domain_id	3ll8B00
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	3ll8C00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Metallo-dependent phosphatases

Domain ID domain_id	3ll8D00
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	86.275 Å
Unit-cell length b length_b	89.699 Å
Unit-cell length c length_c	158.914 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	43.150 Å
R factor r_factor	0.1780
R_work r_work	0.1780
R_free r_free	0.2280

Crystal Structure of Calcineurin in Complex with AKAP79 Peptide

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

AKAP79 peptide

State in the Current Structure

Other States of the Same Protein in the Database

Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform

State in the Current Structure

Other States of the Same Protein in the Database

Calcineurin subunit B type 1

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

3ll8__assembly_3__model_1

3ll8__assembly_3__model_1 | I(q)

3ll8__assembly_3__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (3)

Crystal Structure of Calcineurin in Complex with AKAP79 Peptide

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

AKAP79 peptide

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Calcineurin subunit B type 1

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

3ll8__assembly_3__model_1

3ll8__assembly_3__model_1 | I(q)

3ll8__assembly_3__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (3)