SAXSdb — 5y4f

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

Ankyrin-2

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 430–873	Fragment：UNP RESIDUES 430-873	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.2 M CaCl2, 0.1 M HEPES (pH 7.5), 28% v/v PEG 400	Resolution 1.95 Å R-free 0.220
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 430–873	Fragment：UNP RESIDUES 430-873	CA CALCIUM ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.2 M CaCl2, 0.1 M HEPES (pH 7.5), 28% v/v PEG 400	Resolution 1.95 Å R-free 0.220

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 5Y4F	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4D8O Crystal Structure of the ankyrin-B ZU5-ZU5-UPA-DD tandem Deposited 2012-01-11	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 966–1210（245 aa） Fragment：residues 966-1535 Chain A 1253–1568（316 aa） Fragment：residues 966-1535	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；18% PEG3350, 0.2M ammonium acetate, 5% n-Octyl-beta-D-glucoside, pH 7.5, vapor diffusion, hanging drop, temperature 289K	Resolution 2.20 Å R-free 0.245
4RLV Crystal Structure of AnkB 24 Ankyrin Repeats in Complex with AnkR Autoinhibition Segment Deposited 2014-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–873（846 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；0.5 M ammonium sulfate, 1.0 M lithium sulfate, and 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.49 Å R-free 0.253
4RLY Crystal Structure of AnkB Ankyrin Repeats (R1-R9) in Complex with Nav1.2 Ankyrin Binding Domain Deposited 2014-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–318（291 aa）	Not recorded	SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；1.8 M ammonium sulfate, 6-8% dioxane, and 0.1 M MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.50 Å R-free 0.238
4RLY Crystal Structure of AnkB Ankyrin Repeats (R1-R9) in Complex with Nav1.2 Ankyrin Binding Domain Deposited 2014-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 28–318（291 aa）	Not recorded	SO4 SULFATE ION × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；1.8 M ammonium sulfate, 6-8% dioxane, and 0.1 M MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.50 Å R-free 0.238
5Y4D Crystal Structure of AnkB Ankyrin Repeats in Complex with AnkR/AnkB Chimeric Autoinhibition Segment Deposited 2017-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3707–3718（12 aa） Fragment：UNP RESIDUES 1577-1613,UNP RESIDUES 3707-3718,UNP RESIDUES 28-693 Chain A 28–693（666 aa） Fragment：UNP RESIDUES 1577-1613,UNP RESIDUES 3707-3718,UNP RESIDUES 28-693	Not recorded	SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；4 M ammonium acetate, 0.1 M Bis-Tris propane (pH 7.0)	Resolution 3.30 Å R-free 0.229
5Y4E Crystal Structure of AnkB Ankyrin Repeats R8-14 in complex with autoinhibition segment AI-b Deposited 2017-08-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 857–896（40 aa） Fragment：UNP RESIDUES 857-896,UNP RESIDUES 264-483 Chain A 264–483（220 aa） Fragment：UNP RESIDUES 857-896,UNP RESIDUES 264-483	Not recorded	GOL GLYCEROL × 2 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；0.1 M HEPES (pH 7.0), 1 M ammonium sulfate, 0.5% w/v PEG 8000	Resolution 2.34 Å R-free 0.233
5Y4E Crystal Structure of AnkB Ankyrin Repeats R8-14 in complex with autoinhibition segment AI-b Deposited 2017-08-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 857–896（40 aa） Fragment：UNP RESIDUES 857-896,UNP RESIDUES 264-483 Chain B 264–483（220 aa） Fragment：UNP RESIDUES 857-896,UNP RESIDUES 264-483	Not recorded	SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；0.1 M HEPES (pH 7.0), 1 M ammonium sulfate, 0.5% w/v PEG 8000	Resolution 2.34 Å R-free 0.233
5YIR Crystal Structure of AnkB LIR/GABARAP complex Deposited 2017-10-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1588–1614（27 aa） Fragment：UNP RESIDUES 1588-1614	Not recorded	NI NICKEL (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；12% w/v PEG 3350, 5 mM CoCl2, 5 mM NiCl2, 5 mM CdCl2, 5 mM MgCl2, 0.1 M HEPES buffer (pH 7.5)	Resolution 2.75 Å R-free 0.224
5YIR Crystal Structure of AnkB LIR/GABARAP complex Deposited 2017-10-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1588–1614（27 aa） Fragment：UNP RESIDUES 1588-1614	Not recorded	NI NICKEL (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；12% w/v PEG 3350, 5 mM CoCl2, 5 mM NiCl2, 5 mM CdCl2, 5 mM MgCl2, 0.1 M HEPES buffer (pH 7.5)	Resolution 2.75 Å R-free 0.224
5YIR Crystal Structure of AnkB LIR/GABARAP complex Deposited 2017-10-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1588–1614（27 aa） Fragment：UNP RESIDUES 1588-1614	Not recorded	NI NICKEL (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；12% w/v PEG 3350, 5 mM CoCl2, 5 mM NiCl2, 5 mM CdCl2, 5 mM MgCl2, 0.1 M HEPES buffer (pH 7.5)	Resolution 2.75 Å R-free 0.224
5YIS Crystal Structure of AnkB LIR/LC3B complex Deposited 2017-10-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1588–1614（27 aa） Fragment：UNP RESIDUES 1588-1614	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；289 K；2.4 M ammonium phosphate dibasic, 0.1 M Tris buffer (pH 8.5)	Resolution 2.20 Å R-free 0.250
5YIS Crystal Structure of AnkB LIR/LC3B complex Deposited 2017-10-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1588–1614（27 aa） Fragment：UNP RESIDUES 1588-1614	Not recorded	GOL GLYCEROL × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；289 K；2.4 M ammonium phosphate dibasic, 0.1 M Tris buffer (pH 8.5)	Resolution 2.20 Å R-free 0.250
6KZJ Crystal structure of Ankyrin B/NdeL1 complex Deposited 2019-09-24	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1499–1570（72 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；289 K；1.9M ammonium sulfate, 0.16M potassium sodium tartrate tetrahydrate, 0.1M sodium citrate tribasic dehydrate pH 5.6	Resolution 1.50 Å R-free 0.211
6M3Q Crystal structure of AnkB/beta4-spectrin complex Deposited 2020-03-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 951–1458（508 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；25% w/v pentaerythritol propoxylate 629 (17/8 PO/OH), 50 mM magnesium chloride and 0.1 M HEPES, pH 7.5	Resolution 3.44 Å R-free 0.307
8ZE8 Arf-GTPase activating protein Asap1 SH3 domain in complex with 440 Kd Ankyrin-B fragment Deposited 2024-05-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1699–1710（12 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M MES monohydrate, pH=6.0, 20 % w/v Polyethylene glycol 6,000	Resolution 2.07 Å R-free 0.226
8ZE8 Arf-GTPase activating protein Asap1 SH3 domain in complex with 440 Kd Ankyrin-B fragment Deposited 2024-05-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1699–1710（12 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M MES monohydrate, pH=6.0, 20 % w/v Polyethylene glycol 6,000	Resolution 2.07 Å R-free 0.226
8ZE8 Arf-GTPase activating protein Asap1 SH3 domain in complex with 440 Kd Ankyrin-B fragment Deposited 2024-05-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1699–1710（12 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M MES monohydrate, pH=6.0, 20 % w/v Polyethylene glycol 6,000	Resolution 2.07 Å R-free 0.226
8ZE8 Arf-GTPase activating protein Asap1 SH3 domain in complex with 440 Kd Ankyrin-B fragment Deposited 2024-05-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1699–1710（12 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M MES monohydrate, pH=6.0, 20 % w/v Polyethylene glycol 6,000	Resolution 2.07 Å R-free 0.226

10 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ANK2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–444； UniProt 430–873 Author chain B； PDBConstruct 1–444； UniProt 430–873

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	5y4f
Deposition date deposition_date	2017-08-03
Structure title title	Crystal Structure of AnkB Ankyrin Repeats R13-24 in complex with autoinhibition segment AI-c
Keywords keywords	ANK REPEAT, PROTEIN-PROTEIN INTERACTION, STRUCTURAL PROTEIN, AUTO-INHIBITION, PROTEIN BINDING; PROTEIN BINDING
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	39.46 Å
Radius of gyration Rg (electron density) rg_electron	38.86 Å
Forward intensity I(0) i0	116311000.00
Molecular weight molecular_weight	87005.0 kDa
Excluded volume excluded_volume	109030 Å³
Envelope volume envelope_volume	160680 Å³
Hydration-shell volume shell_volume	34298 Å³
Envelope diameter envelope_diameter	119.8 Å
Shell Rg shell_rg	46.05 Å
Envelope Rg envelope_rg	36.50 Å
Shape Rg shape_rg	38.84 Å
Total Rg total_rg	39.41 Å
Total atoms total_atoms	6117
Residues n_residues	828
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	118.7 Å
Rg (real space) rg_real	39.31 Å
Rg uncertainty (real space) rg_real_error	1.30 Å
I(0) (real space) i0_real	1.1630e+08
I(0) uncertainty (real space) i0_real_error	2.1920e+06
Rg (reciprocal space) rg_reciprocal	39.41 Å
I(0) (reciprocal space) i0_reciprocal	116300000.0000
Solution quality estimate total_estimate	0.8552
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	59.4 Å
Skewness Skewness skewness	-0.042
Kurtosis Kurtosis kurtosis	-0.794
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3577000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.682

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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	Ankyrin-2
Molecular weight formula_weight	47356.7 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	6407

SGLTPIHVAAFMGHLNIVLLLLQNGASPDVTNIRGETALHMAARAGQVEVVRCLLRNGALVDARAREEQTPLHIASRLGKTEIVQLLLQHMAHPDAATTNGYTPLHISAREGQVDVASVLLEAGAAHSLATKKGFTPLHVAAKYGSLDVAKLLLQRRAAADSAGKNGLTPLHVAAHYDNQKVALLLLEKGASPHATAKNGYTPLHIAAKKNQMQIASTLLNYGAETNIVTKQGVTPLHLASQEGHTDMVTLLLDKGANIHMSTKSGLTSLHLAAQEDKVNVADILTKHGADQDAHTKLGYTPLIVACHYGNVKMVNFLLKQGANVNAKTKNGYTPLHQAAQQGHTHIINVLLQHGAKPNATTANGNTALAIAKRLGYISVVDTLKVVTEEVTTTTTTITEKHKLNVPETMTEVLDVSDEEGDDTMTGDGGEYLRPEDLKELGDD

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	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 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	274

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5y4fa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.211 — beta-hairpin-alpha-hairpin repeat
Superfamily Superfamily superfamily	d.211.1 — Ankyrin repeat
Family Family family	d.211.1.0 — automated matches

Domain ID domain_id	d5y4fb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.211 — beta-hairpin-alpha-hairpin repeat
Superfamily Superfamily superfamily	d.211.1 — Ankyrin repeat
Family Family family	d.211.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	5y4fA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

Domain ID domain_id	5y4fB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

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8. Citations (1)

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Unit-cell length a length_a	29.304 Å
Unit-cell length b length_b	127.803 Å
Unit-cell length c length_c	257.550 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	1.953 Å
Low-resolution limit resolution_low	38.161 Å
R factor r_factor	0.1856
R_work r_work	0.1838
R_free r_free	0.2198

fit	/app/data/saxs_computation/y4/5y4f/5y4f.fit
pddf	/app/data/pr_computation/y4/5y4f/5y4f.pr.out
profile	/app/data/saxs_computation/y4/5y4f/5y4f.dat

Crystal Structure of AnkB Ankyrin Repeats R13-24 in complex with autoinhibition segment AI-c

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

Ankyrin-2

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