SAXSdb — 6bnt

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

AP-2 complex subunit mu

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 158–433	Fragment：C-terminal domain (UNP residues 158-433)	Insulin receptor substrate 1 × 1 （P35568）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；1.0 M sodium malonate, pH 5.0, 0.1 M sodium acetate tri-hydrate, pH 4.5, 2% w/v PEG20000	Resolution 3.20 Å R-free 0.234

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 6BNT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6URI HIV-1 Nef in complex with the CD4 cytoplasmic domain and the AP2 clathrin adaptor complex Deposited 2019-10-23	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain M 1–135（135 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 6.9；298 K；15% Peg 4000, 0.2M potassium chloride, ~10% 1,6-hexanediol, 0.1M HEPES	Resolution 3.00 Å R-free 0.277

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

View Construct and Data Evidence

UniProt name	AP2M1_HUMAN
Isoform	Q96CW1-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 40–315； UniProt 158–433

Insulin receptor substrate 1

Homo sapiens

UniProt P35568

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 607–620	Fragment：UNP residues 607-620 Non-standard monomer：Yes (specific site not provided by mmCIF)	AP-2 complex subunit mu × 1 （Q96CW1）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；1.0 M sodium malonate, pH 5.0, 0.1 M sodium acetate tri-hydrate, pH 4.5, 2% w/v PEG20000	Resolution 3.20 Å R-free 0.234

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 6BNT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1IRS IRS-1 PTB DOMAIN COMPLEXED WITH A IL-4 RECEPTOR PHOSPHOPEPTIDE, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-03-22	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 157–267（111 aa） Fragment：PTB DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1K3A Structure of the Insulin-like Growth Factor 1 Receptor Kinase Deposited 2001-10-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 891–902（12 aa）	Not recorded	ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 8000, sodium chloride, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.251
1QQG CRYSTAL STRUCTURE OF THE PH-PTB TARGETING REGION OF IRS-1 Deposited 1999-06-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 4–267（264 aa） Fragment：PH-PTB (N-TERMINAL DOMAIN) Chain B 4–267（264 aa） Fragment：PH-PTB (N-TERMINAL DOMAIN)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；1.7M SODIUM PHOSPHATE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 21K	Resolution 2.30 Å R-free 0.247
2Z8C Phosphorylated insulin receptor tyrosine kinase in complex with (4-{[5-carbamoyl-4-(3-methylanilino)pyrimidin-2-yl]amino}phenyl)acetic acid Deposited 2007-09-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 731–736（6 aa）	Not recorded	S91 [4-({5-(AMINOCARBONYL)-4-[(3-METHYLPHENYL)AMINO]PYRIMIDIN-2-YL}AMINO)PHENYL]ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；PEG 3350, VAPOR DIFFUSION, HANGING DROP	Resolution 3.25 Å R-free 0.292
5U1M Structure of the IRS-1 PTB Domain Bound to the Juxtamembrane Region of the Insulin Receptor Deposited 2016-11-28	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 161–265（105 aa） Fragment：PTB domain (UNP residues 161-265)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；ammonium sulfate	Resolution 1.80 Å
7PPL SHP2 catalytic domain in complex with IRS1 (625-639) phosphopeptide (pTyr-632, pSer-636) Deposited 2021-09-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 625–639（15 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 5 EOH ETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；10% PEG 20000, 100mM HEPES buffer pH 7.5, 50mM EDTA	Resolution 1.53 Å R-free 0.197
7PPM SHP2 catalytic domain in complex with IRS1 (889-901) phosphopeptide (pSer-892, pTyr-896) Deposited 2021-09-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 889–901（13 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；10% PEG 20000, 100mM Citrate buffer pH 5.5, EDTA 50mM	Resolution 1.48 Å R-free 0.196

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IRS1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–15； UniProt 607–620

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	6bnt
Deposition date deposition_date	2017-11-17
Structure title title	Crystal structure of AP2 mu1 adaptin C-terminal domain with IRS-1 peptide
Keywords keywords	AP2 mu1, IRS1, ENDOCYTOSIS; ENDOCYTOSIS
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	24.07 Å
Radius of gyration Rg (electron density) rg_electron	23.63 Å
Forward intensity I(0) i0	14158300.00
Molecular weight molecular_weight	29253.0 kDa
Excluded volume excluded_volume	37091 Å³
Envelope volume envelope_volume	46424 Å³
Hydration-shell volume shell_volume	17949 Å³
Envelope diameter envelope_diameter	88.9 Å
Shell Rg shell_rg	28.49 Å
Envelope Rg envelope_rg	24.01 Å
Shape Rg shape_rg	23.62 Å
Total Rg total_rg	24.34 Å
Total atoms total_atoms	2050
Residues n_residues	256
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	86.0 Å
Rg (real space) rg_real	24.39 Å
Rg uncertainty (real space) rg_real_error	0.85 Å
I(0) (real space) i0_real	1.4160e+07
I(0) uncertainty (real space) i0_real_error	2.2280e+05
Rg (reciprocal space) rg_reciprocal	24.32 Å
I(0) (reciprocal space) i0_reciprocal	14160000.0000
Solution quality estimate total_estimate	0.7716
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.5 Å
Skewness Skewness skewness	0.600
Kurtosis Kurtosis kurtosis	-0.247
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5391000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.570; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.467; Smooth: 0.849

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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	AP-2 complex subunit mu
Molecular weight formula_weight	35697.6 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	2084

MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSEFGRPGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENAIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVIKWVRYIGRSGIYETRC

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Insulin receptor substrate 1
Molecular weight formula_weight	1661.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

CHTDDGYMPMSPGVA

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	34

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6bntA01
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	6bntA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1170 — Mu homology domain, subdomain B

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8. Citations (1)

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Unit-cell length a length_a	125.334 Å
Unit-cell length b length_b	125.334 Å
Unit-cell length c length_c	74.818 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	3.200 Å
Low-resolution limit resolution_low	27.642 Å
R factor r_factor	0.2092
R_work r_work	0.2063
R_free r_free	0.2343

fit	/app/data/saxs_computation/bn/6bnt/6bnt.fit
pddf	/app/data/pr_computation/bn/6bnt/6bnt.pr.out
profile	/app/data/saxs_computation/bn/6bnt/6bnt.dat

Crystal structure of AP2 mu1 adaptin C-terminal domain with IRS-1 peptide

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

AP-2 complex subunit mu

State in the Current Structure

Other States of the Same Protein in the Database

Insulin receptor substrate 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 (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) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)