SAXSdb — 6m3p

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

Ankyrin-3

Rattus norvegicus

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 975–1465	Not recorded	Spectrin beta chain, non-erythrocytic 1 × 1 （Q62261）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；289 K；10% w/v polyethylene glycol 6,000, 5% v/v (+/-)-2-methyl-2,4-pentanediol and 0.1 M HEPES pH 7.5	Resolution 3.31 Å R-free 0.295
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 975–1465	Not recorded	Spectrin beta chain, non-erythrocytic 1 × 1 （Q62261）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；289 K；10% w/v polyethylene glycol 6,000, 5% v/v (+/-)-2-methyl-2,4-pentanediol and 0.1 M HEPES pH 7.5	Resolution 3.31 Å R-free 0.295

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 6M3P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5YIP Crystal Structure of AnkG LIR/GABARAPL1 complex Deposited 2017-10-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1985–2010（26 aa） Fragment：UNP RESIDUES 1985-2010	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；289 K；35% w/v Pentaerythritol ethoxylate 797 (15/4 EO/OH), 0.2 M ammonium sulfate, 0.1 M sodium acetate (pH 4.6)	Resolution 1.85 Å R-free 0.222
5YIQ Crystal structure of AnkG LIR/LC3B complex Deposited 2017-10-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1985–2010（26 aa） Fragment：UNP RESIDUES 1985-2010	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；289 K；10% v/v 2-propanol, 0.2 M zinc acetate, 0.1 M MES buffer (pH 6.5)	Resolution 2.60 Å R-free 0.259
6A9X Crystal Structure of AnkG/GABARAP Complex Deposited 2018-07-16	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1987–2010（24 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；289 K；2.0 M ammonium citrate tribasic, 0.1 M BIS-TRIS propane buffer	Resolution 2.20 Å R-free 0.249
6M3R Crystal structure of AnkG/beta4-spectrin complex Deposited 2020-03-04	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 975–1465（491 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；289 K；0.8 M potassium sodium tartrate tetrahydrate, 0.1 M Tris, pH 8.5 and 0.5% w/v polyethylene glycol monomethyl ether 5,000	Resolution 4.31 Å R-free 0.295
7XCE Crystal structure of Ankyrin G in complex with neurofascin Deposited 2022-03-24	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 275–500（226 aa）	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289.2 K；0.1 M ammonium acetate, 0.1 M Bis-Tris (pH 5.5), 17% w/v polyethylene glycol 10000	Resolution 2.50 Å R-free 0.233

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ANK3_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–491； UniProt 975–1465 Author chain E； PDBConstruct 1–491； UniProt 975–1465

Spectrin beta chain, non-erythrocytic 1

Mus musculus

UniProt Q62261

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1591–1910	Not recorded	Ankyrin-3 × 1 （O70511）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；289 K；10% w/v polyethylene glycol 6,000, 5% v/v (+/-)-2-methyl-2,4-pentanediol and 0.1 M HEPES pH 7.5	Resolution 3.31 Å R-free 0.295
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1591–1910	Not recorded	Ankyrin-3 × 1 （O70511）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；289 K；10% w/v polyethylene glycol 6,000, 5% v/v (+/-)-2-methyl-2,4-pentanediol and 0.1 M HEPES pH 7.5	Resolution 3.31 Å R-free 0.295

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 6M3P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BTN STRUCTURE OF THE BINDING SITE FOR INOSITOL PHOSPHATES IN A PH DOMAIN Deposited 1995-08-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2199–2304（106 aa） Fragment：PH DOMAIN, RESIDUES 2199 - 2304	Not recorded	I3P D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.00 Å R-free 0.286
1MPH PLECKSTRIN HOMOLOGY DOMAIN FROM MOUSE BETA-SPECTRIN, NMR, 50 STRUCTURES Deposited 1997-04-23	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2199–2304（106 aa） Fragment：PLECKSTRIN HOMOLOGY	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K	Resolution not provided

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SPTB2_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–320； UniProt 1591–1910 Author chain B； PDBConstruct 1–320； UniProt 1591–1910

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	6m3p
Deposition date deposition_date	2020-03-04
Structure title title	Crystal structure of AnkG/beta2-spectrin complex
Keywords keywords	PROTEIN BINDING, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
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	53.03 Å
Radius of gyration Rg (electron density) rg_electron	53.31 Å
Forward intensity I(0) i0	323653000.00
Molecular weight molecular_weight	144630.0 kDa
Excluded volume excluded_volume	178980 Å³
Envelope volume envelope_volume	302280 Å³
Hydration-shell volume shell_volume	50220 Å³
Envelope diameter envelope_diameter	212.2 Å
Shell Rg shell_rg	51.88 Å
Envelope Rg envelope_rg	52.10 Å
Shape Rg shape_rg	53.31 Å
Total Rg total_rg	53.28 Å
Total atoms total_atoms	10198
Residues n_residues	1450
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	200.1 Å
Rg (real space) rg_real	53.37 Å
Rg uncertainty (real space) rg_real_error	2.72 Å
I(0) (real space) i0_real	3.2370e+08
I(0) uncertainty (real space) i0_real_error	7.3290e+06
Rg (reciprocal space) rg_reciprocal	52.73 Å
I(0) (reciprocal space) i0_reciprocal	323400000.0000
Solution quality estimate total_estimate	0.8463
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	60.0 Å
Skewness Skewness skewness	0.470
Kurtosis Kurtosis kurtosis	-0.201
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14810000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.735; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.896; Smooth: 0.896

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Ankyrin-3
Molecular weight formula_weight	54560.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,C
Atom count atom_count	10198

ADTLDNVNLVSSPVHSGFLVSFMVDARGGSMRGSRHHGMRIIIPPRKCTAPTRITCRLVKRHKLANPPPMVEGEGLASRLVEMGPAGAQFLGPVIVEIPHFGSMRGKERELIVLRSENGETWKEHQFDSKNEDLSELLNGMDEELDSPEELGTKRICRIITKDFPQYFAVVSRIKQESNQIGPEGGILSSTTVPLVQASFPEGALTKRIRVGLQAQPVPEETVKKILGNKATFSPIVTVEPRRRKFHKPITMTIPVPPPSGEGVSNGYKGDTTPSLRLLCSITGGTSPAQWEDITGTTPLTFIKDCVSFTTNVSARFWLADCHQVLETVGLASQLYRELICVPYMAKFVVFAKTNDPVESSLRCFCMTDDRVDKTLEQQENFEEVARSKDIEVLEGKPIYVDCYGNLAPLTKGGQQLVFNFYSFKENRLPFSIKVRDTSQEPCGRLSFLKEPKTTKGLPQTAVCNLNITLPAHKKAEKADRRQSFTSLALR

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Spectrin beta chain, non-erythrocytic 1
Molecular weight formula_weight	37066.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

AHKAQQYYFDAAEAEAWMSEQELYMMSEEKAKDEQSAVSMLKKHQILEQAVEDYAETVHQLSKTSRALVADSHPESERISMRQSKVDKLYAGLKDLAEERRGKLDERHRLFQLNREVDDLEQWIAEREVVAGSHELGQDYEHVTMLQERFREFARDTGNIGQERVDTVNNMADELINSGHSDAATIAEWKDGLNEAWADLLELIDTRTQILAASYELHKFYHDAKEIFGRIQDKHKKLPEELGRDQNTVETLQRMHTTFEHDIQALGTQVRQLQEDAARLQAAYAGDKADDIQKRENEVLEAWKSLLDACEGRRVRLVDT

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	6m3pA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	6m3pB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	6m3pC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	220 — Chondroitinase Ac; Chain A, domain 3
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	6m3pC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	220 — Chondroitinase Ac; Chain A, domain 3
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	6m3pC03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2660 —

Domain ID domain_id	6m3pE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	220 — Chondroitinase Ac; Chain A, domain 3
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	6m3pE02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	220 — Chondroitinase Ac; Chain A, domain 3
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	6m3pE03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2660 —

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8. Citations (1)

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Unit-cell length a length_a	66.277 Å
Unit-cell length b length_b	66.305 Å
Unit-cell length c length_c	160.926 Å
Unit-cell angle α angle_alpha	99.47 °
Unit-cell angle β angle_beta	99.78 °
Unit-cell angle γ angle_gamma	100.87 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.312 Å
Low-resolution limit resolution_low	44.995 Å
R factor r_factor	0.2563
R_work r_work	0.2545
R_free r_free	0.2951

fit	/app/data/saxs_computation/m3/6m3p/6m3p.fit
pddf	/app/data/pr_computation/m3/6m3p/6m3p.pr.out
profile	/app/data/saxs_computation/m3/6m3p/6m3p.dat

Crystal structure of AnkG/beta2-spectrin complex

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

Ankyrin-3

State in the Current Structure

Other States of the Same Protein in the Database

Spectrin beta chain, non-erythrocytic 1

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)