SAXSdb — 5z7l

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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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 10–126 Chain B； UniProt 10–126	Fragment：UNP residues 10-126	5-azacytidine-induced protein 2 × 2 （Q9H6S1） 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

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 5Z7L	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 mutation/modification Different oligomeric state 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 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 mutation/modification 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 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification 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 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
5AAQ TBK1 recruitment to cytosol-invading Salmonella induces anti- bacterial autophagy Deposited 2015-07-28	Different construct Different mutation/modification Different oligomeric state 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 388–446（59 aa） Fragment：UNP RESIDUES 388-446	Not recorded	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
5Z7A Crystal structure of NDP52 SKICH region Deposited 2018-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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
7EAA crystal structure of NDP52 SKICH domain in complex with RB1CC1 coiled-coil domain Deposited 2021-03-06	Different construct Different ligand/ion 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 1–117； UniProt 10–126 Author chain B； PDBConstruct 1–117； UniProt 10–126

5-azacytidine-induced protein 2

Homo sapiens

UniProt Q9H6S1

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 33–75 Chain D； UniProt 33–75	Fragment：UNP residues 33-75	Calcium-binding and coiled-coil domain-containing protein 2 × 2 （Q13137） 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

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 5Z7L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5EP6 The crystal structure of NAP1 in complex with TBK1 Deposited 2015-11-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 215–255（41 aa） Fragment：UNP RESIDUES 215-255	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291.15 K；1% w/v Tryptone, 0.05 M HEPES sodium (pH 7.0), 12% w/v PEG 3350	Resolution 1.45 Å R-free 0.217
5EP6 The crystal structure of NAP1 in complex with TBK1 Deposited 2015-11-11	Different construct Different mutation/modification 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 215–255（41 aa） Fragment：UNP RESIDUES 215-255	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291.15 K；1% w/v Tryptone, 0.05 M HEPES sodium (pH 7.0), 12% w/v PEG 3350	Resolution 1.45 Å R-free 0.217
5Z7G Crystal structure of TAX1BP1 SKICH region in complex with NAP1 Deposited 2018-01-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 33–75（43 aa） Chain D 33–75（43 aa）	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；PEG 8000, 0.1 M HEPES	Resolution 2.30 Å R-free 0.233
7EA2 crystal structure of NAP1 FIR in complex with RB1CC1 Claw domain Deposited 2021-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 6–16（11 aa） Chain B 6–16（11 aa）	Not recorded	P6G HEXAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2 FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M phosphate/citrate pH 4.2, 40% PEG300	Resolution 2.14 Å R-free 0.232

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AZI2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–43； UniProt 33–75 Author chain D； PDBConstruct 1–43； UniProt 33–75

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	5z7l
Deposition date deposition_date	2018-01-29
Structure title title	Crystal structure of NDP52 SKICH region in complex with NAP1
Keywords keywords	NDP52, NAP1, SKICH, Autophagy, SIGNALING PROTEIN; SIGNALING 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	24.31 Å
Radius of gyration Rg (electron density) rg_electron	23.67 Å
Forward intensity I(0) i0	21539900.00
Molecular weight molecular_weight	36718.0 kDa
Excluded volume excluded_volume	46521 Å³
Envelope volume envelope_volume	57349 Å³
Hydration-shell volume shell_volume	21219 Å³
Envelope diameter envelope_diameter	80.6 Å
Shell Rg shell_rg	29.33 Å
Envelope Rg envelope_rg	24.26 Å
Shape Rg shape_rg	23.62 Å
Total Rg total_rg	24.60 Å
Total atoms total_atoms	2601
Residues n_residues	305
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	77.7 Å
Rg (real space) rg_real	24.34 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	2.1540e+07
I(0) uncertainty (real space) i0_real_error	3.0990e+05
Rg (reciprocal space) rg_reciprocal	24.33 Å
I(0) (reciprocal space) i0_reciprocal	21540000.0000
Solution quality estimate total_estimate	0.9016
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.4 Å
Skewness Skewness skewness	0.293
Kurtosis Kurtosis kurtosis	-0.575
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6495000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.981

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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	Calcium-binding and coiled-coil domain-containing protein 2
Molecular weight formula_weight	14015.9 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	2882

TSAVLLDHCHFSQVIFNSVEKFYIPGGDVTCHYTFTQHFIPRRKDWIGIFRVGWKTTREYYTFMWVTLPIDLNNKSAKQQEVQFKAYYLPKDDEYYQFCYVDEDGVVRGASIPFQFR

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-Pichia pastoris shuttle vector pPpARG4

Entity 2 Entity 2 polymer

Description description	5-azacytidine-induced protein 2
Molecular weight formula_weight	5058.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

ESVASHFALVTAYEDIKKRLKDSEKENSLLKKRIRFLEEKLIA

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-Pichia pastoris shuttle vector pPpARG4

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	272

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5z7lA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2840 —

Domain ID domain_id	5z7lB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2840 —

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8. Citations (1)

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Unit-cell length a length_a	113.639 Å
Unit-cell length b length_b	45.026 Å
Unit-cell length c length_c	86.679 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	123.77 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.020 Å
Low-resolution limit resolution_low	40.645 Å
R factor r_factor	0.1727
R_work r_work	0.1703
R_free r_free	0.2216

fit	/app/data/saxs_computation/z7/5z7l/5z7l.fit
pddf	/app/data/pr_computation/z7/5z7l/5z7l.pr.out
profile	/app/data/saxs_computation/z7/5z7l/5z7l.dat

Crystal structure of NDP52 SKICH region in complex with NAP1

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

5-azacytidine-induced 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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)