SAXSdb — 4be8

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

E3 UBIQUITIN-PROTEIN LIGASE NEDD4

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 519–900	Fragment：HECT DOMAIN, RESIDUES 519-900 Mutation：YES	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 9；1.15 M POTASSIUM SODIUM TARTRATE, 0.1 M TRIS-HCL, PH 9.0	Resolution 3.00 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 4BE8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2KPZ Human NEDD4 3RD WW Domain Complex with The Human T-cell Leukemia virus 1 GAG-Pro poliprotein Derived Peptide SDPQIPPPYVEP Deposited 2009-10-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 834–878（45 aa） Fragment：3rd WW Domain, UNP residues 834-878	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；288 K；Pressure ambient NMR sample composition 1 mM [U-100% 15N] PROTEIN-1; 3 mM PEPTIDE-2; 20 mM sodium phosphate-3; 0.02 v/v sodium azide-4; 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] PROTEIN-5; 3 mM PEPTIDE-6; 20 mM sodium phosphate-7; 0.02 v/v sodium azide-8; 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KQ0 Human NEDD4 3rd WW Domain Complex with Ebola Zaire Virus Matrix Protein VP40 Derived Peptide ILPTAPPEYMEA Deposited 2009-10-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 834–878（45 aa） Fragment：3rd WW Domain, UNP residues 834-878	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；288 K；Pressure ambient NMR sample composition 1mM [U-100% 15N] PROTEIN; 10mM PEPTIDE; 20mM sodium phosphate; 0.02 v/v % sodium azide; 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2M3O Structure and dynamics of a human Nedd4 WW domain-ENaC complex Deposited 2013-01-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain W 838–877（40 aa） Fragment：third WW domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient NMR sample composition 1.1 mM [U-99% 13C; U-99% 15N] Nedd4 WW3* domain, 2.2 mM alpha ENaC PY peptide, 20 mM sodium phosphate, 0.1 % sodium azide, 1 mM TSP, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 3.0 mM Nedd4 WW3* domain, 1.5 mM [U-99% 13C; U-99% 15N] alpha ENaC PY peptide, 20 mM sodium phosphate, 0.1 % sodium azide, 1.0 mM TSP, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 1.61 mM [U-99% 15N] Nedd4 WW3* domain, 4.38 mM alpha ENaC PY peptide, 20 mM sodium phosphate, 0.1 % sodium azide, 1 mM TSP, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided
2XBB Nedd4 HECT:Ub complex Deposited 2010-04-08	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 519–900（382 aa） Fragment：HECT DOMAIN, RESIDUES 519-900	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；100 MM NA-HEPES, PH 7.5, 10% PEG 2000 MME, 5 MM TCEP.	Resolution 2.68 Å R-free 0.249
2XBB Nedd4 HECT:Ub complex Deposited 2010-04-08	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 B 519–900（382 aa） Fragment：HECT DOMAIN, RESIDUES 519-900	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；100 MM NA-HEPES, PH 7.5, 10% PEG 2000 MME, 5 MM TCEP.	Resolution 2.68 Å R-free 0.249
2XBF Nedd4 HECT structure Deposited 2010-04-09	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 519–900（382 aa） Fragment：HECT DOMAIN, RESIDUES 519-900	Not recorded	EDO 1,2-ETHANEDIOL × 4 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；100 MM NA-MES, PH 6.0, 4% PEG 400, 35 MM CACL2, 5 MM TCEP	Resolution 2.50 Å R-free 0.256
3B7Y Crystal structure of the C2 Domain of the E3 Ubiquitin-Protein Ligase NEDD4 Deposited 2007-10-31	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 101–252（152 aa） Fragment：C2 Domain: Residues 101-252	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；10% PEG 4000, 0.1 M Succinic acid pH 7.0, 0.01M Spermine tetra-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.80 Å R-free 0.209
3B7Y Crystal structure of the C2 Domain of the E3 Ubiquitin-Protein Ligase NEDD4 Deposited 2007-10-31	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 101–252（152 aa） Fragment：C2 Domain: Residues 101-252	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；10% PEG 4000, 0.1 M Succinic acid pH 7.0, 0.01M Spermine tetra-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.80 Å R-free 0.209
4BBN NEDD4 HECT-Ub:Ub complex Deposited 2012-09-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 892–1318（427 aa） Fragment：HECT DOMAIN, RESIDUES 892-1318	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；2.5 SODIUM MALONATE, PH 6.0	Resolution 2.51 Å R-free 0.224
4N7F Crystal structure of 3rd WW domain of human Nedd4-1 Deposited 2013-10-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 841–874（34 aa） Fragment：WW3 domain (UNP residues 841-874)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；3.0M NaCl, 100mM Tris-HCl 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.10 Å R-free 0.200
4N7F Crystal structure of 3rd WW domain of human Nedd4-1 Deposited 2013-10-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 841–874（34 aa） Fragment：WW3 domain (UNP residues 841-874)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；3.0M NaCl, 100mM Tris-HCl 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.10 Å R-free 0.200
4N7H Crystal Structure of the Complex of 3rd WW domain of Human Nedd4 and 1st PPXY Motif of ARRDC3 Deposited 2013-10-15	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 840–872（33 aa） Fragment：3rd WW domain (UNP residues 840-872)	Not recorded	GAI GUANIDINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；0.35M (NH4)SO4, 100mM Tris-HCl 8.0, 100mM Guanidine-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.70 Å R-free 0.233
5AHT Third WW domain from the E3 ubiquitin-protein ligase NEDD4 Deposited 2015-02-09	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 838–877（40 aa） Fragment：WW3, UNP RESIDUES 838-877	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure 1.0 NMR sample composition 1.5 MM [U-99% 13C NMR sample composition U-99% 15N] NEDD4 WW3* DOMAIN, 20 MM SODIUM PHOSPHATE, 50 MM SODIUM CHLORIDE, 0.5 MM DSS, 90% 2O/10% D2O	Resolution not provided
5C7J CRYSTAL STRUCTURE OF NEDD4 WITH A UB VARIANT Deposited 2015-06-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 520–900（381 aa） Fragment：HECT DOMAIN (UNP RESIDUES 520-900)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；The NEDD4 and Ubiquitin Variant was mixed at molar ratio ~1:2, and then concentrated to 15mg/ml. The protein sample was mixed with Trypsin at a 1:1000 (W/W) Trypsin:protein ratio before setting up crystallization. Crystal was initially obtained from Molecular Dimentions Proplex screen condition E04. Crystal used for structure refinement was grown in 20% PEG8000, 10% Glycerol, 0.1M HEPES pH 7.0 in hanging drop setup, using 1.5uL protein, 1.5uL well solution over 0.5 mL reservoir buffer at 20 C. Crystals grow to mountable size in 4 days. Harvested crystal was flash-frozen in liquid nitrogen. 20% Glycerol was used as the cryo-protectant	Resolution 3.00 Å R-free 0.277
5C7J CRYSTAL STRUCTURE OF NEDD4 WITH A UB VARIANT Deposited 2015-06-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 520–900（381 aa） Fragment：HECT DOMAIN (UNP RESIDUES 520-900)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；The NEDD4 and Ubiquitin Variant was mixed at molar ratio ~1:2, and then concentrated to 15mg/ml. The protein sample was mixed with Trypsin at a 1:1000 (W/W) Trypsin:protein ratio before setting up crystallization. Crystal was initially obtained from Molecular Dimentions Proplex screen condition E04. Crystal used for structure refinement was grown in 20% PEG8000, 10% Glycerol, 0.1M HEPES pH 7.0 in hanging drop setup, using 1.5uL protein, 1.5uL well solution over 0.5 mL reservoir buffer at 20 C. Crystals grow to mountable size in 4 days. Harvested crystal was flash-frozen in liquid nitrogen. 20% Glycerol was used as the cryo-protectant	Resolution 3.00 Å R-free 0.277
5C91 NEDD4 HECT with covalently bound indole-based inhibitor Deposited 2015-06-26	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 938–1312（375 aa） Fragment：unp residues 938-1312	Not recorded	4YU methyl (2E)-4-{[(5-methoxy-1,2-dimethyl-1H-indol-3-yl)carbonyl]amino}but-2-enoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, 35 mM calcium chloride, 5 mM TCEP, 6% PEG400	Resolution 2.44 Å R-free 0.298
9H9O Crystal structure of NEDD4 HECT domain in complex with norclomipramine Deposited 2024-10-31	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 519–893（375 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4 A1ITH Norclomipramine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES pH 6.0 8-10% PEG 400 20% glycerol 1-4 mM inhibitor (0.25-1% DMSO)	Resolution 2.12 Å R-free 0.236
9H9T Crystal structure of NEDD4 HECT domain in complex with covalent inhibitor Deposited 2024-10-31	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 519–893（375 aa）	Not recorded	A1ITT ethyl 4-[4-(2-chloranyl-5,6-dihydrobenzo[b][1]benzazepin-11-yl)butylamino]butanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES pH 6.0 8-10% PEG 400 20% glycerol 1-4 mM inhibitor (0.25-1% DMSO)	Resolution 2.17 Å R-free 0.252

14 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NEDD4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–385； UniProt 519–900

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	4be8
Deposition date deposition_date	2013-03-06
Structure title title	NEDD4 HECT A889F structure
Keywords keywords	LIGASE; LIGASE
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	23.96 Å
Radius of gyration Rg (electron density) rg_electron	22.86 Å
Forward intensity I(0) i0	31591900.00
Molecular weight molecular_weight	44097.0 kDa
Excluded volume excluded_volume	55586 Å³
Envelope volume envelope_volume	66478 Å³
Hydration-shell volume shell_volume	24673 Å³
Envelope diameter envelope_diameter	79.6 Å
Shell Rg shell_rg	29.58 Å
Envelope Rg envelope_rg	23.08 Å
Shape Rg shape_rg	22.86 Å
Total Rg total_rg	23.73 Å
Total atoms total_atoms	3121
Residues n_residues	378
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	76.2 Å
Rg (real space) rg_real	23.90 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	3.1590e+07
I(0) uncertainty (real space) i0_real_error	3.8360e+05
Rg (reciprocal space) rg_reciprocal	23.91 Å
I(0) (reciprocal space) i0_reciprocal	31590000.0000
Solution quality estimate total_estimate	0.9017
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.4 Å
Skewness Skewness skewness	0.264
Kurtosis Kurtosis kurtosis	-0.464
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9468000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.958

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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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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4be8a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.148 — Hect, E3 ligase catalytic domain
Superfamily Superfamily superfamily	d.148.1 — Hect, E3 ligase catalytic domain
Family Family family	d.148.1.0 — automated matches

Domain ID domain_id	d4be8a2
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 (3 domains)

Domain ID domain_id	4be8A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1750 — Hect, E3 ligase catalytic domain fold
Homologous superfamily homologous superfamily	10 — Hect, E3 ligase catalytic domains

Domain ID domain_id	4be8A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2160 — Hect, E3 ligase catalytic domain
Homologous superfamily homologous superfamily	10 — Hect, E3 ligase catalytic domain

Domain ID domain_id	4be8A03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2410 — Hect, E3 ligase catalytic fold
Homologous superfamily homologous superfamily	10 — Hect, E3 ligase catalytic domain

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8. Citations (1)

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Unit-cell length a length_a	100.545 Å
Unit-cell length b length_b	100.545 Å
Unit-cell length c length_c	96.450 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.996 Å
Low-resolution limit resolution_low	44.580 Å
R factor r_factor	0.2482
R_work r_work	0.2457
R_free r_free	0.2950

Description description	E3 UBIQUITIN-PROTEIN LIGASE NEDD4
Molecular weight formula_weight	45707.0 kDa
EC 编号 ec_number	6.3.2.-
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3124

NEDD4 HECT A889F structure

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

E3 UBIQUITIN-PROTEIN LIGASE NEDD4

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 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3

fit	/app/data/saxs_computation/be/4be8/4be8.fit
pddf	/app/data/pr_computation/be/4be8/4be8.pr.out
profile	/app/data/saxs_computation/be/4be8/4be8.dat