SAXSdb — 5aaq

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

CALCIUM-BINDING AND COILED-COIL DOMAIN-CONTAINING PROTEIN 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 388–446	Fragment：UNP RESIDUES 388-446	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1.0 NMR sample composition：95% WATER/5% D2O	Resolution not provided

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 5AAQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2MXP Solution structure of NDP52 ubiquitin-binding zinc finger Deposited 2015-01-12	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 414–446（33 aa） Fragment：C-terminal, UNP residues 414-446	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] entity_1-1, 1 mM [U-100% 15N] entity_1-2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] entity_1-3, 100% D2O \| 100% D2O NMR sample composition 1.2 mM entity_1-4, 100% D2O \| 100% D2O	Resolution not provided
3VVV Skich domain of NDP52 Deposited 2012-07-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 21–141（121 aa） Fragment：UNP residues 21-141	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；24% PEG4000, 0.1M Tris , pH 8.5, VAPOR DIFFUSION, temperature 293K	Resolution 1.35 Å R-free 0.189
3VVV Skich domain of NDP52 Deposited 2012-07-28	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–141（121 aa） Fragment：UNP residues 21-141	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；24% PEG4000, 0.1M Tris , pH 8.5, VAPOR DIFFUSION, temperature 293K	Resolution 1.35 Å R-free 0.189
3VVW NDP52 in complex with LC3C Deposited 2012-07-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 21–141（121 aa） Fragment：UNP residues 21-141	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；16% PEG6000, 0.01M sodium citrate , pH 7.0, Vapor Diffusion, temperature 293K	Resolution 2.50 Å R-free 0.252
4GXL The crystal structure of Galectin-8 C-CRD in complex with NDP52 Deposited 2012-09-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 368–381（14 aa） Fragment：UNP residues 368-381	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；283 K；2% PEG 400, 0.1M HEPES sodium pH 7.5, 2.0M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 283K	Resolution 2.02 Å R-free 0.216
4HAN Crystal structure of Galectin 8 with NDP52 peptide Deposited 2012-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 372–385（14 aa） Fragment：UNP residues 372-385 Chain D 372–385（14 aa） Fragment：UNP residues 372-385	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 PEG DI(HYDROXYETHYL)ETHER × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1M Tris-Hcl pH8.5, 30~34% (v/w) PEG400, 200mM LiSO4, and 10mM Nicotinamide adenine dinucleotide, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.55 Å R-free 0.214
4XKL Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin Deposited 2015-01-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 414–446（33 aa） Fragment：Zinc finger, UNP residues 414-446	Not recorded	GOL GLYCEROL × 1 ACT ACETATE ION × 2 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.2 M magnesium acetate tetrahydrate, 20% w/v Polyethylene glycol 3350	Resolution 2.10 Å R-free 0.243
4XKL Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin Deposited 2015-01-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 414–446（33 aa） Fragment：Zinc finger, UNP residues 414-446	Not recorded	GOL GLYCEROL × 1 ACT ACETATE ION × 2 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.2 M magnesium acetate tetrahydrate, 20% w/v Polyethylene glycol 3350	Resolution 2.10 Å R-free 0.243
5Z7A Crystal structure of NDP52 SKICH region Deposited 2018-01-27	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–126（126 aa） Fragment：UNP residues 1-126	Not recorded	SO4 SULFATE ION × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；289 K；PEG 3350, 0.2 M potassium sulfate	Resolution 2.38 Å R-free 0.263
5Z7A Crystal structure of NDP52 SKICH region Deposited 2018-01-27	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–126（126 aa） Fragment：UNP residues 1-126	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；289 K；PEG 3350, 0.2 M potassium sulfate	Resolution 2.38 Å R-free 0.263
5Z7L Crystal structure of NDP52 SKICH region in complex with NAP1 Deposited 2018-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 10–126（117 aa） Fragment：UNP residues 10-126 Chain B 10–126（117 aa） Fragment：UNP residues 10-126	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；PEG3350,sodium malonate	Resolution 2.02 Å R-free 0.222
7EAA crystal structure of NDP52 SKICH domain in complex with RB1CC1 coiled-coil domain Deposited 2021-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 10–141（132 aa） Chain B 10–141（132 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M MgCl2, 0.1 M MES pH 6.0, 8% PEG6000	Resolution 2.60 Å R-free 0.253

9 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CACO2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–60； UniProt 388–446

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	5aaq
Deposition date deposition_date	2015-07-28
Structure title title	TBK1 recruitment to cytosol-invading Salmonella induces anti- bacterial autophagy
Keywords keywords	CALCIUM-BINDING PROTEIN, TBK1, NDP52, ZINC-FINGER; CALCIUM-BINDING PROTEIN
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	16.93 Å
Radius of gyration Rg (electron density) rg_electron	16.70 Å
Forward intensity I(0) i0	271486000.00
Molecular weight molecular_weight	132280.0 kDa
Excluded volume excluded_volume	163300 Å³
Envelope volume envelope_volume	57906 Å³
Hydration-shell volume shell_volume	22293 Å³
Envelope diameter envelope_diameter	71.4 Å
Shell Rg shell_rg	28.30 Å
Envelope Rg envelope_rg	22.42 Å
Shape Rg shape_rg	16.63 Å
Total Rg total_rg	17.47 Å
Total atoms total_atoms	17980
Residues n_residues	1140
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	66.6 Å
Rg (real space) rg_real	17.04 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	2.7150e+08
I(0) uncertainty (real space) i0_real_error	4.4420e+06
Rg (reciprocal space) rg_reciprocal	17.03 Å
I(0) (reciprocal space) i0_reciprocal	271500000.0000
Solution quality estimate total_estimate	0.7990
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.8 Å
Skewness Skewness skewness	0.322
Kurtosis Kurtosis kurtosis	-0.367
Angular range angular_range	— – 0.4700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	80710.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.662; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.408; Smooth: 0.989

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	CALCIUM-BINDING AND COILED-COIL DOMAIN-CONTAINING PROTEIN 2
Molecular weight formula_weight	6800.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	17980

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

TBK1 recruitment to cytosol-invading Salmonella induces anti- bacterial autophagy

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

CALCIUM-BINDING AND COILED-COIL DOMAIN-CONTAINING PROTEIN 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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/aa/5aaq/5aaq.fit
pddf	/app/data/pr_computation/aa/5aaq/5aaq.pr.out
profile	/app/data/saxs_computation/aa/5aaq/5aaq.dat