SAXSdb — 6ncn

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

Apolipoprotein E

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 20–181	Not recorded	KJM 1-(3-chlorophenyl)cyclobutane-1-carboximidamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；296 K；20% w/v Polyethylene glycol monomethyl ether mesylate 5,000; 0.1M Bis-Tris buffer at pH6.5	Resolution 1.82 Å R-free 0.219

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 6NCN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B68 APOLIPOPROTEIN E4 (APOE4), 22K FRAGMENT Deposited 1999-01-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–209（191 aa） Fragment：22K FRAGMENT, ISOFORM E4, RECEPTOR BINDING DOMAIN, RESIDUES 1-191	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；WELL : 28% PEG 400, 20MM NAOAC, PH 6.0, 0.1% BME PROTEIN SOLN: 40MM (NH4)H(CO3), 7MG/ML PROTEIN DROPS : WELL/PROTEIN 1/3, ROOM TEMPERATURE, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.255
1BZ4 APOLIPOPROTEIN E3 (APO-E3), TRUNCATION MUTANT 165 Deposited 1998-11-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 40–183（144 aa） Fragment：22K FRAGMENT, RECEPTOR BINDING DOMAIN, RESIDUES 1-165, TRUNCATION AT RESIDUE 165	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；RT, 50MM NA-CACODYLATE, PH 5.6, 20-25% PEG 400, 1% 2-ME. NOTE : W/O 2-ME, ANOTHER ORTHORHOMBIC FORM APPEARS (SEE PDB ENTRY 1oR2).	Resolution 1.85 Å R-free 0.245
1EA8 Apolipoprotein E3 22kD fragment LYS146GLU mutant Deposited 2001-07-11	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 19–209（191 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 1-191	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；50MM NA-CACODYLATE, PH 5.6, ORTHORHOMBIC FORM ORTHO-2 APPEARS (SEE PDB ENTRY 1OR2).	Resolution 1.95 Å R-free 0.258
1GS9 Apolipoprotein E4, 22k domain Deposited 2002-01-02	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 19–183（165 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 1-165	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；50MM NA-CACODYLATE, PH 5.6, 20-25% PEG 400, 1% 2-ME, RT, CRYSTALLIZED FROM FULL LENGTH APOE4 CONSTRUCT (299 RESIDUES). PROTEOLYTIC CLEAVAGE IN CRYSTALLIZATION DROP TO 22K FRAGMENT. NEW, THIRD ORTHOGONAL CRYSTAL FORM OF APOE (ORTHO-3)	Resolution 1.70 Å R-free 0.247
1H7I Apolipoprotein E3 22kD fragment LYS146GLN mutant Deposited 2001-07-08	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 19–209（191 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 1-191	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；50MM NA-CACODYLATE, PH 5.6, 20-25% PEG 400, 1% 2-ME. RT. ORTHORHOMBIC FORM ORTHO-2 APPEARS (SEE PDB ENTRY 1OR2).	Resolution 1.90 Å R-free 0.259
1LE2 STRUCTURAL BASIS FOR ALTERED FUNCTION IN THE COMMON MUTANTS OF HUMAN APOLIPOPROTEIN-E Deposited 1991-08-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 41–184（144 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
1LE4 STRUCTURAL BASIS FOR ALTERED FUNCTION IN THE COMMON MUTANTS OF HUMAN APOLIPOPROTEIN-E Deposited 1991-08-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 41–184（144 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1LPE THREE-DIMENSIONAL STRUCTURE OF THE LDL RECEPTOR-BINDING DOMAIN OF HUMAN APOLIPOPROTEIN E Deposited 1991-08-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 41–184（144 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.25 Å
1NFN APOLIPOPROTEIN E3 (APOE3) Deposited 1996-07-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–209（191 aa） Fragment：22KD RECEPTOR BINDING DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å R-free 0.259
1NFO APOLIPOPROTEIN E2 (APOE2, D154A MUTATION) Deposited 1996-07-17	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 19–209（191 aa） Fragment：22KD RECEPTOR BINDING DOMAIN	Mutation：D154A	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.270
1OEF PEPTIDE OF HUMAN APOE RESIDUES 263-286, NMR, 5 STRUCTURES AT PH 4.8, 37 DEGREES CELSIUS AND PEPTIDE:SDS MOLE RATIO OF 1:90 Deposited 1996-03-16	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 281–304（24 aa） Fragment：RESIDUES 263 - 286	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.8；310 K	Resolution not provided
1OEG PEPTIDE OF HUMAN APOE RESIDUES 267-289, NMR, 5 STRUCTURES AT PH 6.0, 37 DEGREES CELSIUS AND PEPTIDE:SDS MOLE RATIO OF 1:90 Deposited 1996-03-16	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 285–307（23 aa） Fragment：RESIDUES 267 - 289	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；310 K	Resolution not provided
1OR2 APOLIPOPROTEIN E3 (APOE3) TRUNCATION MUTANT 165 Deposited 1999-03-25	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 19–183（165 aa） Fragment：RECEPTOR BINDING DOMAIN, RESIDUES 1-165	Mutation：TRUNCATION AT RESIDUE 165 Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；50MM NA-CACODYLATE, PH 5.6, 10-20% PEG 400 AT ROOM TEMPERATURE. NO 2-ME ADDED. NOTE: WITH 2-ME OR LOWER PEG CONCENTRATIONS, OTHER CRYSTAL FORMS APPEARS (SEE PDB ENTRIES 1BZ4, 1OR3), VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.297
1OR3 APOLIPOPROTEIN E3 (APOE3), TRIGONAL TRUNCATION MUTANT 165 Deposited 1998-12-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–183（165 aa） Fragment：RECEPTOR BINDING DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；RT, 50MM NA-CACODYLATE, PH 5.6, 10-20% PEG 400, 1% 2-ME. NOTE: W/O 2-ME OR HIGHER PEG CONCENTRATIONS, OTHER CRYSTAL FORMS APPEARS (SEE PDB ENTRIES 1BZ4, 1OR2).	Resolution 1.73 Å R-free 0.238
2KC3 NMR solution structure of complete receptor binding domain of human apolipoprotein E Deposited 2008-12-15	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 19–201（183 aa） Fragment：UNP residues 19-201	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N; U-70% 2H] Human apolipoprotein E N-terminal domain-1, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N; U-30% 2H] Human apolipoprotein E N-terminal domain-2, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2KNY Fusion construct of CR17 from LRP-1 and ApoE residues 130-149 Deposited 2009-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 147–167（21 aa） Fragment：Fusion of LRP UNP residues 2770-2817 and Apo-E UNP residues 147-167	Not recorded	CA CALCIUM ION × 1	SOLUTION NMR NMR measurement conditions pH 7.45；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR measurement conditions pH 7.45；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR sample composition 20 mM [U-99% 2H] HEPES-1, 50 mM sodium chloride-2, 3 mM sodium azide-3, 5 mM CALCIUM ION-4, 0.8 mM [U-99% 13C; U-99% 15N] entity_1-5, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 20 mM [U-99% 2H] HEPES-6, 50 mM sodium chloride-7, 3 mM sodium azide-8, 5 mM CALCIUM ION-9, 0.8 mM [U-99% 13C; U-99% 15N] entity_1-10, 100% D2O \| 100% D2O NMR sample composition 20 mM [U-99% 2H] HEPES-11, 50 mM sodium chloride-12, 3 mM sodium azide-13, 5 mM CALCIUM ION-14, 0.8 mM [U-99% 15N] entity_1-15, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 20 mM [U-99% 2H] HEPES-16, 150 mM sodium chloride-17, 3 mM sodium azide-18, 2 mM [U-99% 2H] EDTA-19, 0.5 mM [U-99% 15N] entity_2-20, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 20 mM [U-99% 2H] HEPES-21, 150 mM sodium chloride-22, 3 mM sodium azide-23, 2 mM [U-99% 2H] EDTA-24, 0.5 mM [U-99% 13C; U-99% 15N] entity_2-25, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2L7B NMR Structure of full length apoE3 Deposited 2010-12-07	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 19–317（299 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.9；303 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 1 mM [U-13C; U-15N; U-2H] apoE3, 100 mM sodium phosphate, 10 mM DTT, 5 mM [U-100% 2H] EDTA, 1 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N; U-50% 2H] apoE3, 10 mM DTT, 1 mM DSS, 5 mM [U-100% 2H] EDTA, 100 mM sodium phosphate, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6IWB Crystal structure of a computationally designed protein (LD3) in complex with BCL-2 Deposited 2018-12-05	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 A 41–186（146 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295.15 K；17% PEG2000, 0.1M Sodium Succinate (pH 5.5), 0.32M Ammonium Sulfate	Resolution 2.50 Å R-free 0.275
6IWB Crystal structure of a computationally designed protein (LD3) in complex with BCL-2 Deposited 2018-12-05	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 41–186（146 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295.15 K；17% PEG2000, 0.1M Sodium Succinate (pH 5.5), 0.32M Ammonium Sulfate	Resolution 2.50 Å R-free 0.275
6NCO Fragment-based Discovery of an apoE4 Stabilizer Deposited 2018-12-11	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–181（162 aa）	Not recorded	KQP 1-[5-chloro-4'-(2-hydroxypropan-2-yl)[1,1'-biphenyl]-3-yl]cyclobutane-1-carboximidamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；296 K；20% w/v Polyethylene glycol monomethyl ether mesylate 5,000; 0.1M Bis-Tris buffer at pH6.5	Resolution 1.71 Å R-free 0.220
6V7M Crystal structure of a proteolytically cleaved, amino terminal domain of apolipoprotein E3 Deposited 2019-12-08	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 1–100（100 aa） Fragment：UNP residues 1-100 Chain B 101–183（83 aa） Fragment：UNP residues 101-183	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；298 K；Crystallization was by sitting drop vapor diffusion in Cryschem plates at room temperature. Reservoirs were 16% to 18 % 2-methyl-2,4-pentanediol (MPD) buffered with 0.1 M sodium acetate at pH 5.8 and including 0.25% octyl-beta-D-1-thioglucopyranoside. The droplets were initial composed of equal amounts of the reservoir and an 8 mg/ml solution of the protein in 0.02 M ammonium carbonate.	Resolution 2.00 Å R-free 0.260
7FCR Crystal structure of the N-terminal domain of mutants of Human Apolipoprotein-E (ApoE) Deposited 2021-07-15	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 19–209（191 aa）	Mutation：C130I	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 5.15；294 K；100 mM sodium cacodylate, 28% PEG 400	Resolution 1.40 Å R-free 0.194
7FCS Crystal structure of the N-terminal domain of mutants of Human Apolipoprotein-E (ApoE) Deposited 2021-07-15	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 19–209（191 aa）	Mutation：C130V	NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 5.15；294 K；100 mM sodium cacodylate, 28% PEG 400	Resolution 1.60 Å R-free 0.216
7UVJ Rationally Designed ED1 Epitope-Scaffold Immunogen for SARS-CoV-2 Deposited 2022-05-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 40–183（144 aa）	Not recorded	GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；0.2 M sodium formate, 20% w/v PEG3350	Resolution 1.99 Å R-free 0.312
7UVJ Rationally Designed ED1 Epitope-Scaffold Immunogen for SARS-CoV-2 Deposited 2022-05-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 40–183（144 aa）	Not recorded	GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；0.2 M sodium formate, 20% w/v PEG3350	Resolution 1.99 Å R-free 0.312
8AX8 Human Apolipoprotein E4 (ApoE4) N-terminal domain (space group P3121) Deposited 2022-08-31	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 19–317（299 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；HEPES, PEG3350	Resolution 1.55 Å R-free 0.231
8AX9 Human Apolipoprotein E4 (ApoE4) N-terminal domain (space group P212121) Deposited 2022-08-31	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 19–317（299 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；HEPES, PEG3350	Resolution 1.55 Å R-free 0.195
8CDY N-terminal domain of human apolipoprotein E Deposited 2023-02-01	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 19–317（299 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；HEPES, PEG 6000	Resolution 1.90 Å R-free 0.231
8CE0 N-terminal domain of human apolipoprotein E Deposited 2023-02-01	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 19–317（299 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；NaCl, Hepes, PEG 8000	Resolution 1.75 Å R-free 0.215
8GRX APOE4 receptor in complex with APOE4 NTD Deposited 2022-09-02	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 41–180（140 aa） Chain C 41–180（140 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

28 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	APOE_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–182； UniProt 20–181

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	6ncn
Deposition date deposition_date	2018-12-11
Structure title title	Fragment-based Discovery of an apoE4 Stabilizer
Keywords keywords	Lipid Binding Lipid Transport, LIPID TRANSPORT; LIPID 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	18.71 Å
Radius of gyration Rg (electron density) rg_electron	18.04 Å
Forward intensity I(0) i0	5590240.00
Molecular weight molecular_weight	16779.0 kDa
Excluded volume excluded_volume	20900 Å³
Envelope volume envelope_volume	24551 Å³
Hydration-shell volume shell_volume	12699 Å³
Envelope diameter envelope_diameter	68.2 Å
Shell Rg shell_rg	22.49 Å
Envelope Rg envelope_rg	18.67 Å
Shape Rg shape_rg	18.04 Å
Total Rg total_rg	18.82 Å
Total atoms total_atoms	1178
Residues n_residues	141
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	68.8 Å
Rg (real space) rg_real	18.93 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	5.5900e+06
I(0) uncertainty (real space) i0_real_error	7.3070e+04
Rg (reciprocal space) rg_reciprocal	18.90 Å
I(0) (reciprocal space) i0_reciprocal	5590000.0000
Solution quality estimate total_estimate	0.7687
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.9 Å
Skewness Skewness skewness	0.663
Kurtosis Kurtosis kurtosis	0.054
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1555000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.457; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.631; Smooth: 0.987

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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	Apolipoprotein E
Molecular weight formula_weight	21523.2 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	1329

GSSHHHHHHSSGLVPRGSHMKVEQAVETEPEPELRQQTEWQSGQRWELALGRFWDYLRWVQTLSEQVQEELLSSQVTQELRALMDETMKELKAYKSELEEQLTPVAEETRARLSKELQAAQARLGADMEDVRGRLVQYRGEVQAMLGQSTEELRVRLASHLRKLRKRLLRDADDLQKRLAVYQAG

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	1-(3-chlorophenyl)cyclobutane-1-carboximidamide
Molecular weight formula_weight	208.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	129

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6ncna1
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.1 — Apolipoprotein
Family Family family	a.24.1.1 — Apolipoprotein

Domain ID domain_id	d6ncna2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	6ncnA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	20 — Apolipoprotein

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8. Citations (1)

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Unit-cell length a length_a	41.070 Å
Unit-cell length b length_b	52.790 Å
Unit-cell length c length_c	84.540 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.820 Å
Low-resolution limit resolution_low	36.940 Å
R factor r_factor	0.1852
R_work r_work	0.1836
R_free r_free	0.2192

fit	/app/data/saxs_computation/nc/6ncn/6ncn.fit
pddf	/app/data/pr_computation/nc/6ncn/6ncn.pr.out
profile	/app/data/saxs_computation/nc/6ncn/6ncn.dat

Fragment-based Discovery of an apoE4 Stabilizer

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

Apolipoprotein E

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