SAXSdb — 3vvw

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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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 21–141	Fragment：UNP residues 21-141	Microtubule-associated proteins 1A/1B light chain 3C × 1 （Q9BXW4）	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

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 3VVW	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 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 oligomeric state 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 oligomeric state 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
4GXL The crystal structure of Galectin-8 C-CRD in complex with NDP52 Deposited 2012-09-04	Different construct 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 mutation/modification Different oligomeric state 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 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 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 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 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 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
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 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 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 3–123； UniProt 21–141

Microtubule-associated proteins 1A/1B light chain 3C

Homo sapiens

UniProt Q9BXW4

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 B； UniProt 1–126	Fragment：UNP residues 1-126	Calcium-binding and coiled-coil domain-containing protein 2 × 1 （Q13137）	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

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 3VVW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NCN Solution Structure of the Autophagy-Related Protein LC3C Deposited 2016-04-11	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 1–126（126 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；293.15 K；Ionic strength (raw mmCIF value) 171；Pressure 1 NMR sample composition 0.35-0.7 mM [U-15N] Microtubule-associated protein light chain 3C (LC3C), 20 mM PIPES, 150 mM sodium chloride, 0.1 mM EDTA, 2% [U-2H] glycerol, 90% H2O, 10% D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.35-0.7 mM [U-13C; U-15N] Microtubule-associated protein light chain 3C (LC3C), 20 mM PIPES, 150 mM sodium chloride, 0.1 mM EDTA, 2% [U-2H] glycerol, 90% H2O, 10% D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.35-0.7 mM [U-13C; U-15N] Microtubule-associated protein light chain 3C (LC3C), 20 mM PIPES, 150 mM sodium chloride, 0.1 mM EDTA, 2% [U-2H] glycerol, 100% D2O, 100% D2O \| 100% D2O	Resolution not provided
3WAM Crystal structure of human LC3C_8-125 Deposited 2013-05-06	Different construct 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 8–125（118 aa） Fragment：UNP RESIDUES 8-125	Not recorded	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；0.5M di-Ammonium hydrogen citrate, 10% PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.75 Å R-free 0.211
3WAM Crystal structure of human LC3C_8-125 Deposited 2013-05-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 8–125（118 aa） Fragment：UNP RESIDUES 8-125	Not recorded	CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；0.5M di-Ammonium hydrogen citrate, 10% PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.75 Å R-free 0.211
3WAP Crystal structure of Atg13 LIR-fused human LC3C_8-125 Deposited 2013-05-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 8–125（118 aa） Fragment：UNP RESIDUES 436-447, 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；0.1M Sodium acetate trihydrate, 8% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.10 Å R-free 0.273
3WAP Crystal structure of Atg13 LIR-fused human LC3C_8-125 Deposited 2013-05-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 8–125（118 aa） Fragment：UNP RESIDUES 436-447, 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；0.1M Sodium acetate trihydrate, 8% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.10 Å R-free 0.273
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 8–125（118 aa） Fragment：UNP residues 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 8–125（118 aa） Fragment：UNP residues 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 8–125（118 aa） Fragment：UNP residues 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 8–125（118 aa） Fragment：UNP residues 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 8–125（118 aa） Fragment：UNP residues 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 8–125（118 aa） Fragment：UNP residues 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 8–125（118 aa） Fragment：UNP residues 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246
5DPW Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125 Deposited 2015-09-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 8–125（118 aa） Fragment：UNP residues 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；278 K；0.2 M Potassium Phosphate monobasic, 20% w/v Polyethylene glycol 3,350	Resolution 2.19 Å R-free 0.246

4 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MLP3C_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–128； UniProt 1–126

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	3vvw
Deposition date deposition_date	2012-07-28
Structure title title	NDP52 in complex with LC3C
Keywords keywords	autophagy adaptor protein, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	24.92 Å
Radius of gyration Rg (electron density) rg_electron	24.46 Å
Forward intensity I(0) i0	11050200.00
Molecular weight molecular_weight	26301.0 kDa
Excluded volume excluded_volume	33418 Å³
Envelope volume envelope_volume	42016 Å³
Hydration-shell volume shell_volume	15615 Å³
Envelope diameter envelope_diameter	83.9 Å
Shell Rg shell_rg	29.05 Å
Envelope Rg envelope_rg	24.60 Å
Shape Rg shape_rg	24.44 Å
Total Rg total_rg	25.17 Å
Total atoms total_atoms	1861
Residues n_residues	224
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	83.9 Å
Rg (real space) rg_real	25.26 Å
Rg uncertainty (real space) rg_real_error	0.82 Å
I(0) (real space) i0_real	1.1050e+07
I(0) uncertainty (real space) i0_real_error	1.7010e+05
Rg (reciprocal space) rg_reciprocal	25.19 Å
I(0) (reciprocal space) i0_reciprocal	11050000.0000
Solution quality estimate total_estimate	0.6686
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	20.0 Å
Skewness Skewness skewness	0.470
Kurtosis Kurtosis kurtosis	-0.679
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3129000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.478; Stabil: 0.959; Sysdev: 1.000; Positv: 1.000; Valcen: 0.375; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Calcium-binding and coiled-coil domain-containing protein 2
Molecular weight formula_weight	14598.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1902

GPSQVIFNSVEKFYIPGGDVTCHYTFTQHFIPRRKDWIGIFRVGWKTTREYYTFMWVTLPIDLNNKSAKQQEVQFKAYYLPKDDEYYQFCYVDEDGVVRGASIPFQFRPENEEDILVVTTQGE

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 polymer

Description description	Microtubule-associated proteins 1A/1B light chain 3C
Molecular weight formula_weight	14812.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPMPPPQKIPSVRPFKQRKSLAIRQEEVAGIRAKFPNKIPVVVERYPRETFLPPLDKTKFLVPQELTMTQFLSIIRSRMVLRATEAFYLLVNNKSLVSMSATMAEIYRDYKDEDGFVYMTYASQETFG

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	41

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3vvwb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3vvwA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2840 —

Domain ID domain_id	3vvwB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	195.720 Å
Unit-cell length b length_b	37.420 Å
Unit-cell length c length_c	40.280 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.66 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	40.147 Å
R factor r_factor	0.2121
R_work r_work	0.2101
R_free r_free	0.2520

fit	/app/data/saxs_computation/vv/3vvw/3vvw.fit
pddf	/app/data/pr_computation/vv/3vvw/3vvw.pr.out
profile	/app/data/saxs_computation/vv/3vvw/3vvw.dat

NDP52 in complex with LC3C

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

Microtubule-associated proteins 1A/1B light chain 3C

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)