SAXSdb — 7bn1

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

Clathrin heavy chain 1

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 1–364	Not recorded	Protein mu-NS from Reovirus type 1 × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；297 K；30% PEG 550 MME; PEG 20K, 0.12M Monosaccharides (D-Glucose; D-Mannose; D-Galactose; L-Fucose; D-Xylose; N-Acetyl-D-Glucosamine) and 0.1M Sodium HEPES; MOPS (acid) pH-7.5	Resolution 1.97 Å R-free 0.215
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–364	Not recorded	Protein mu-NS from Reovirus type 1 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；297 K；30% PEG 550 MME; PEG 20K, 0.12M Monosaccharides (D-Glucose; D-Mannose; D-Galactose; L-Fucose; D-Xylose; N-Acetyl-D-Glucosamine) and 0.1M Sodium HEPES; MOPS (acid) pH-7.5	Resolution 1.97 Å R-free 0.215

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 7BN1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2XZG Clathrin Terminal Domain Complexed with Pitstop 1 Deposited 2010-11-25	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 1–364（364 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1-364	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2 GOL GLYCEROL × 1 ACT ACETATE ION × 1 VH1 2-(4-AMINOBENZYL)-1,3-DIOXO-2,3-DIHYDRO-1H-BENZO[DE]ISOQUINOLINE-5-SULFONATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；20% PEG 3350, 150 MM POTASSIUM ACETATE, 0.1 M TRIS, PH 8.0.	Resolution 1.70 Å R-free 0.200
4G55 Clathrin terminal domain complexed with pitstop 2 Deposited 2012-07-17	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 1–364（364 aa） Fragment：N-TERMINAL DOMAIN	Not recorded	DMS DIMETHYL SULFOXIDE × 4 ACT ACETATE ION × 5 EDO 1,2-ETHANEDIOL × 6 PEG DI(HYDROXYETHYL)ETHER × 2 VH2 N-[5-[(4-BROMOPHENYL)METHYL]-4-HYDROXY-1,3-THIAZOL-2-YL]NAPHTHALENE-1-SULFONAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；20% PEG 3350, 150 MM POTASSIUM ACETATE, 0.1 M TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.69 Å R-free 0.215
6E4L The structure of the N-terminal domain of human clathrin heavy chain 1 (nTD) in complex with ES9 Deposited 2018-07-17	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 1–364（364 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 2 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 2 ACT ACETATE ION × 3 HRS 5-bromo-N-(4-nitrophenyl)thiophene-2-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；20% PEG 3350, 150 MM POTASSIUM ACETATE, 0.1 M TRIS, pH 8.0	Resolution 1.60 Å R-free 0.214
6QNN CLATHRIN HEAVY CHAIN N-TERMINAL DOMAIN BOUND TO GTSE1 LIDL MOTIF Deposited 2019-02-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–364（364 aa） Fragment：;LIDL motifs A-E, REFSEQ RESIDUES 661-726, N-TERMINAL 'GPLG' ARE NON-NATURAL ;	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；20% PEG 6000, 0.1M TRIS pH 8.0	Resolution 2.03 Å R-free 0.284
6QNP CLATHRIN HEAVY CHAIN N-TERMINAL DOMAIN BOUND TO GTSE1 LIDL MOTIF Deposited 2019-02-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–364（364 aa） Fragment：;LIDL motifs A-D, REFSEQ RESIDUES 653-719, N-TERMINAL 'GPLGS' ARE NON-NATURAL ;	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；12% PEG 4000, 0.1M SODIUM ACETATE, 0.1M HEPES pH 7.0	Resolution 2.70 Å R-free 0.291
6QNP CLATHRIN HEAVY CHAIN N-TERMINAL DOMAIN BOUND TO GTSE1 LIDL MOTIF Deposited 2019-02-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–364（364 aa） Fragment：;LIDL motifs A-D, REFSEQ RESIDUES 653-719, N-TERMINAL 'GPLGS' ARE NON-NATURAL ;	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；12% PEG 4000, 0.1M SODIUM ACETATE, 0.1M HEPES pH 7.0	Resolution 2.70 Å R-free 0.291
6QNP CLATHRIN HEAVY CHAIN N-TERMINAL DOMAIN BOUND TO GTSE1 LIDL MOTIF Deposited 2019-02-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–364（364 aa） Fragment：;LIDL motifs A-D, REFSEQ RESIDUES 653-719, N-TERMINAL 'GPLGS' ARE NON-NATURAL ;	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；12% PEG 4000, 0.1M SODIUM ACETATE, 0.1M HEPES pH 7.0	Resolution 2.70 Å R-free 0.291
6QNP CLATHRIN HEAVY CHAIN N-TERMINAL DOMAIN BOUND TO GTSE1 LIDL MOTIF Deposited 2019-02-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–364（364 aa） Fragment：;LIDL motifs A-D, REFSEQ RESIDUES 653-719, N-TERMINAL 'GPLGS' ARE NON-NATURAL ;	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；12% PEG 4000, 0.1M SODIUM ACETATE, 0.1M HEPES pH 7.0	Resolution 2.70 Å R-free 0.291
7BN2 Clathrin heavy chain N-terminal domain bound to Non structured protein 3 from Eastern Equine Encephalitis Virus Deposited 2021-01-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain AAA 1–364（364 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；30% PEG 550 MME; PEG 20K and 0.1M NPS buffer system NaN03; Na2HPO4; (NH4)2SO4, pH-6.5	Resolution 1.97 Å R-free 0.219
7BN2 Clathrin heavy chain N-terminal domain bound to Non structured protein 3 from Eastern Equine Encephalitis Virus Deposited 2021-01-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain BBB 1–364（364 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；30% PEG 550 MME; PEG 20K and 0.1M NPS buffer system NaN03; Na2HPO4; (NH4)2SO4, pH-6.5	Resolution 1.97 Å R-free 0.219
7ZX4 Clathrin N-terminal domain in complex with a HURP phospho-peptide Deposited 2022-05-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–364（364 aa）	Not recorded	GOL GLYCEROL × 2 CL CHLORIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；50 mM Tris pH 7.5, 30 % PEG 6000	Resolution 2.08 Å R-free 0.249
7ZX4 Clathrin N-terminal domain in complex with a HURP phospho-peptide Deposited 2022-05-20	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–364（364 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；50 mM Tris pH 7.5, 30 % PEG 6000	Resolution 2.08 Å R-free 0.249
9C0Y Clathrin terminal domain complexed with Pitstop 2c Deposited 2024-05-28	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 1–364（364 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 2 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 3 ACT ACETATE ION × 2 A1ATR N-{(5Z)-4-oxo-5-[(2-phenoxyphenyl)methylidene]-4,5-dihydro-1,3-thiazol-2-yl}naphthalene-2-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 3350, 150 MM POTASSIUM ACETATE, 0.1 M TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature	Resolution 1.40 Å R-free 0.206
9C0Z Clathrin terminal domain complexed with pitstop 2d Deposited 2024-05-28	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 2–364（363 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 ACT ACETATE ION × 2 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1 A1ATQ ~{N}-[4-oxidanylidene-5-[(2-phenoxyphenyl)methylidene]-1,3-thiazol-2-yl]naphthalene-1-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 3350, 150 MM POTASSIUM ACETATE, 0.1 M TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.51 Å R-free 0.186

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

View Construct and Data Evidence

UniProt name	CLH1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–364； UniProt 1–364 Author chain B； PDBConstruct 1–364； UniProt 1–364

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	7bn1
Deposition date deposition_date	2021-01-21
Structure title title	Clathrin heavy chain N-terminal domain complexed with peptide from Protein mu-NS of Reovirus type 1
Keywords keywords	CLTC-NTD, Clathrin-Box motif, Viral Replication protein E1, HPV, TRANSPORT PROTEIN; TRANSPORT 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	31.46 Å
Radius of gyration Rg (electron density) rg_electron	30.92 Å
Forward intensity I(0) i0	105004000.00
Molecular weight molecular_weight	82092.0 kDa
Excluded volume excluded_volume	103210 Å³
Envelope volume envelope_volume	128620 Å³
Hydration-shell volume shell_volume	35786 Å³
Envelope diameter envelope_diameter	113.3 Å
Shell Rg shell_rg	36.67 Å
Envelope Rg envelope_rg	31.02 Å
Shape Rg shape_rg	30.90 Å
Total Rg total_rg	31.49 Å
Total atoms total_atoms	5767
Residues n_residues	738
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	108.0 Å
Rg (real space) rg_real	31.60 Å
Rg uncertainty (real space) rg_real_error	0.85 Å
I(0) (real space) i0_real	1.0500e+08
I(0) uncertainty (real space) i0_real_error	1.6060e+06
Rg (reciprocal space) rg_reciprocal	31.54 Å
I(0) (reciprocal space) i0_reciprocal	105000000.0000
Solution quality estimate total_estimate	0.8608
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.4 Å
Skewness Skewness skewness	0.463
Kurtosis Kurtosis kurtosis	-0.372
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	20000000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.756; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.969

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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	Clathrin heavy chain 1
Molecular weight formula_weight	40543.5 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	6282

MAQILPIRFQEHLQLQNLGINPANIGFSTLTMESDKFICIREKVGEQAQVVIIDMNDPSNPIRRPISADSAIMNPASKVIALKAGKTLQIFNIEMKSKMKAHTMTDDVTFWKWISLNTVALVTDNAVYHWSMEGESQPVKMFDRHSSLAGCQIINYRTDAKQKWLLLTGISAQQNRVVGAMQLYSVDRKVSQPIEGHAASFAQFKMEGNAEESTLFCFAVRGQAGGKLHIIEVGTPPTGNQPFPKKAVDVFFPPEAQNDFPVAMQISEKHDVVFLITKYGYIHLYDLETGTCIYMNRISGETIFVTAPHEATAGIIGVNRKGQVLSVCVEEENIIPYITNVLQNPDLALRMAVRNNLAGAEELF

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	Protein mu-NS from Reovirus type 1
Molecular weight formula_weight	1826.9 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

VDGAADLIDFSVPTDEY

Entity 3 Entity 3 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	465

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8. Citations (1)

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Unit-cell length a length_a	137.533 Å
Unit-cell length b length_b	128.932 Å
Unit-cell length c length_c	78.100 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.50 °
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	1.970 Å
Low-resolution limit resolution_low	89.430 Å
R factor r_factor	0.1854
R_work r_work	0.1839
R_free r_free	0.2154

fit	/app/data/saxs_computation/bn/7bn1/7bn1.fit
pddf	/app/data/pr_computation/bn/7bn1/7bn1.pr.out
profile	/app/data/saxs_computation/bn/7bn1/7bn1.dat

Clathrin heavy chain N-terminal domain complexed with peptide from Protein mu-NS of Reovirus type 1

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

Clathrin heavy chain 1

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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)