SAXSdb — 1hes

▼

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

CLATHRIN COAT ASSEMBLY PROTEIN AP50

RATTUS NORVEGICUS

UniProt P20172

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 158–435	Fragment：INTERNALIZATION SIGNAL BINDING DOMAIN	P-SELECTIN PEPTIDE × 1 （P16109）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.1；289 K；HANGING DROP, 2.2M NACL, 0.4M NA/K PHOSPHATE, 10MM DTT 0.1M MES PH 7.1, 15% GLYCEROL, 16 DEGREES, MOLAR RATIO OF PEPTIDE TO PROTEIN 3:1	Resolution 3.00 Å R-free 0.266

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 1HES	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1H6E MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH CTLA-4 INTERNALIZATION PEPTIDE TTGVYVKMPPT Deposited 2001-06-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 164–435（272 aa） Fragment：INTERNALIZATION SIGNAL BINDING DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；HANGING DROPS CONTAINING A 1:1 MIXTURE OF COMPLEX SOLUTION 6MG/ML PROTEIN AND 1MM 11MER PEPTIDE SOLUTION IN 20MM HEPES PH7.5, 1MM DTT AND RESERVOIR BUFFER 1.4-2.4M SODIUM CHLORIDE, 0.1M MES PH6.2-7.0, 0.4M NA/K PHOSPHATE, 15% GLYCEROL, pH 7.00	Resolution 3.60 Å R-free 0.317

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AP50_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–285； UniProt 158–435

P-SELECTIN PEPTIDE

OrganismNot specified

UniProt P16109

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 P； UniProt 813–830	Fragment：INTERNALIZATION SIGNAL	CLATHRIN COAT ASSEMBLY PROTEIN AP50 × 1 （P20172）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.1；289 K；HANGING DROP, 2.2M NACL, 0.4M NA/K PHOSPHATE, 10MM DTT 0.1M MES PH 7.1, 15% GLYCEROL, 16 DEGREES, MOLAR RATIO OF PEPTIDE TO PROTEIN 3:1	Resolution 3.00 Å R-free 0.266

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 1HES	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FSB STRUCTURE OF THE EGF DOMAIN OF P-SELECTIN, NMR, 19 STRUCTURES Deposited 1996-03-25	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 160–199（40 aa） Fragment：EGF DOMAIN, RESIDUES 119 - 158	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K	Resolution not provided
1G1Q Crystal structure of P-selectin lectin/EGF domains Deposited 2000-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 42–199（158 aa） Fragment：LECTIN/EGF DOMAINS Chain B 42–199（158 aa） Fragment：LECTIN/EGF DOMAINS Chain C 42–199（158 aa） Fragment：LECTIN/EGF DOMAINS Chain D 42–199（158 aa） Fragment：LECTIN/EGF DOMAINS	Not recorded	CA CALCIUM ION × 4 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Tris-HCl, NaCl, CaCl2, 2-methyl-2,4-pentanediol, PEG 6000, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 291K	Resolution 2.40 Å R-free 0.252
1G1R Crystal structure of P-selectin lectin/EGF domains complexed with SLeX Deposited 2000-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 42–199（158 aa） Fragment：LECTIN/EGF DOMAINS Chain B 42–199（158 aa） Fragment：LECTIN/EGF DOMAINS Chain C 42–199（158 aa） Fragment：LECTIN/EGF DOMAINS Chain D 42–199（158 aa） Fragment：LECTIN/EGF DOMAINS	Not recorded	CA CALCIUM ION × 4 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Tris-HCl, NaCl, CaCl2, 2-methyl-2,4-pentanediol, PEG 6000, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 291K	Resolution 3.40 Å R-free 0.322
1G1S P-SELECTIN LECTIN/EGF DOMAINS COMPLEXED WITH PSGL-1 PEPTIDE Deposited 2000-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 42–199（158 aa） Fragment：LECTIN/EGF DOMAINS Chain B 42–199（158 aa） Fragment：LECTIN/EGF DOMAINS	Not recorded	SR STRONTIUM ION × 2 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 7 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；100 mM HEPES, 10 mM TRIS, 150 mN NaCl, 4 mM CaCl2, 50 mM SrCl2, 5% PEG 6000, 33% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 291K	Resolution 1.90 Å R-free 0.235

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

View Construct and Data Evidence

UniProt name	LEM3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 1–18； UniProt 813–830

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1hes
Deposition date deposition_date	2000-11-24
Structure title title	MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH P-selectin INTERNALIZATION PEPTIDE SHLGTYGVFTNAA
Keywords keywords	ENDOCYTOSIS/EXOCYTOSIS, ENDOCYTOSIS, ADAPTOR, PEPTIDE COMPLEX, PEPTIDE BINDING PROTE, ENDOCYTOSIS-EXOCYTOSIS complex; ENDOCYTOSIS/EXOCYTOSIS
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.09 Å
Radius of gyration Rg (electron density) rg_electron	23.64 Å
Forward intensity I(0) i0	14486400.00
Molecular weight molecular_weight	29964.0 kDa
Excluded volume excluded_volume	38115 Å³
Envelope volume envelope_volume	47040 Å³
Hydration-shell volume shell_volume	18112 Å³
Envelope diameter envelope_diameter	89.6 Å
Shell Rg shell_rg	28.70 Å
Envelope Rg envelope_rg	24.29 Å
Shape Rg shape_rg	23.63 Å
Total Rg total_rg	24.39 Å
Total atoms total_atoms	2105
Residues n_residues	265
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	87.7 Å
Rg (real space) rg_real	24.42 Å
Rg uncertainty (real space) rg_real_error	0.90 Å
I(0) (real space) i0_real	1.4490e+07
I(0) uncertainty (real space) i0_real_error	2.3250e+05
Rg (reciprocal space) rg_reciprocal	24.34 Å
I(0) (reciprocal space) i0_reciprocal	14490000.0000
Solution quality estimate total_estimate	0.7653
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	86.3 Å
Skewness Skewness skewness	0.622
Kurtosis Kurtosis kurtosis	-0.185
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4678000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.542; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.421; Smooth: 0.897

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	CLATHRIN COAT ASSEMBLY PROTEIN AP50
Molecular weight formula_weight	32758.4 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	2138

MHHHHHHQIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENAIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVIKWVRYIGRSGIYETRC

来源 Source

来源生物 organism	RATTUS NORVEGICUS
通用名 common_name	NORWAY RAT
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	ESCHERICHIA COLI BL21

Entity 2 Entity 2 polymer

Description description	P-SELECTIN PEPTIDE
Molecular weight formula_weight	1882.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

SHLGTYGVFTNAAFDPSP

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	33

▼

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1hesa_
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.7 — Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor
Family Family family	b.2.7.1 — Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor

CATH v4.4 (2 domains)

Domain ID domain_id	1hesA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1170 — Mu homology domain, subdomain B

Domain ID domain_id	1hesA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1170 — Mu homology domain, subdomain B

▶

8. Citations (2)

▶

Unit-cell length a length_a	125.720 Å
Unit-cell length b length_b	125.720 Å
Unit-cell length c length_c	75.270 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 64
Space-group number int_tables_number	172
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	100.000 Å
R factor r_factor	0.2130
R_work r_work	0.2100
R_free r_free	0.2660

fit	/app/data/saxs_computation/he/1hes/1hes.fit
pddf	/app/data/pr_computation/he/1hes/1hes.pr.out
profile	/app/data/saxs_computation/he/1hes/1hes.dat

MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH P-selectin INTERNALIZATION PEPTIDE SHLGTYGVFTNAA

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

CLATHRIN COAT ASSEMBLY PROTEIN AP50

State in the Current Structure

Other States of the Same Protein in the Database

P-SELECTIN PEPTIDE

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)