SAXSdb — 2khn

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

Intersectin-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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–111	Fragment：UNP residues 1-111	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 430；Pressure ambient NMR sample composition：0.87 mM [U-98% 13C; U-98% 15N] HR3646E-1, 20 mM MES-2, 200 mM sodium chloride-3, 5 mM calcium chloride-4, 10 mM DTT-5, 0.02 % sodium azide-6, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.81 mM [U-5% 13C; U-98% 15N] HR3646E-7, 20 mM MES-8, 200 mM sodium chloride-9, 5 mM calcium chloride-10, 10 mM DTT-11, 0.02 % sodium azide-12, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

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 2KHN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1KI1 Guanine Nucleotide Exchange Region of Intersectin in Complex with Cdc42 Deposited 2001-12-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1229–1581（353 aa） Fragment：Dbl homology and Pleckstrin homology domains (residues 1229-1580)	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；PEG 4000, ammonium sulfate, Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.30 Å R-free 0.247
1KI1 Guanine Nucleotide Exchange Region of Intersectin in Complex with Cdc42 Deposited 2001-12-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1229–1581（353 aa） Fragment：Dbl homology and Pleckstrin homology domains (residues 1229-1580)	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；PEG 4000, ammonium sulfate, Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.30 Å R-free 0.247
2KGR Solution structure of protein ITSN1 from Homo sapiens. Northeast Structural Genomics Consortium target HR5524A Deposited 2009-03-16	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 210–312（103 aa） Fragment：residues 210-312	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.2；Pressure ambient NMR sample composition 1.0 mM [U-100% 13C; U-100% 15N] protein-1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM [U-5% 13C; U-99% 15N] protein-2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3FIA Crystal structure of the EH 1 domain from human intersectin-1 protein. Northeast Structural Genomics Consortium target HR3646e. Deposited 2008-12-11	Different construct Different mutation/modification 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 1–111（111 aa） Fragment：residues 1-111	Mutation：M1V, I14T Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions microbatch under oil；pH 8.5；277 K；1.5M ammonium sulfate, 12% glycerol, 0.1M TrisHCl, pH 8.5, microbatch under oil , temperature 277K	Resolution 1.45 Å R-free 0.176
3QBV Structure of designed orthogonal interaction between CDC42 and nucleotide exchange domains of intersectin Deposited 2011-01-14	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 × 2 PDB declaration: dimeric	Chain B 1229–1579（351 aa） Fragment：DH AND PH DOMAINS (UNP Residues 1229-1571)	Mutation：S1373E	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；100mm TRIS pH 7.5, 25% PEG 3350, 150mm ammonium sulfate, and 1mM DTT, temperature 295k, VAPOR DIFFUSION, HANGING DROP	Resolution 2.65 Å R-free 0.284
3QBV Structure of designed orthogonal interaction between CDC42 and nucleotide exchange domains of intersectin Deposited 2011-01-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1229–1579（351 aa） Fragment：DH AND PH DOMAINS (UNP Residues 1229-1571)	Mutation：S1373E	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；100mm TRIS pH 7.5, 25% PEG 3350, 150mm ammonium sulfate, and 1mM DTT, temperature 295k, VAPOR DIFFUSION, HANGING DROP	Resolution 2.65 Å R-free 0.284
4IIM Crystal structure of the Second SH3 Domain of ITSN1 bound with a synthetic peptide Deposited 2012-12-20	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 × 5 PDB declaration: pentameric	Chain A 916–970（55 aa） Chain B 916–970（55 aa）	Not recorded	UNX UNKNOWN LIGAND × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；1.2 M NaCitrate and 0.1 M Tris, pH 8.5, vapor diffusion hanging drop, temperature 291K	Resolution 1.80 Å R-free 0.243
4IIM Crystal structure of the Second SH3 Domain of ITSN1 bound with a synthetic peptide Deposited 2012-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 916–970（55 aa） Chain B 916–970（55 aa）	Not recorded	UNX UNKNOWN LIGAND × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；1.2 M NaCitrate and 0.1 M Tris, pH 8.5, vapor diffusion hanging drop, temperature 291K	Resolution 1.80 Å R-free 0.243
5HZI Crystal structure of photoinhibitable Intersectin1 containing C450M mutant LOV2 domain Deposited 2016-02-02	Different construct Different mutation/modification 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 1230–1308（79 aa） Chain A 1238–1509（272 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.5, 9% (w/v) PEG 8000, 9% (v/v) ethylene glycol	Resolution 2.60 Å R-free 0.285
5HZI Crystal structure of photoinhibitable Intersectin1 containing C450M mutant LOV2 domain Deposited 2016-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1230–1308（79 aa） Chain B 1238–1509（272 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.5, 9% (w/v) PEG 8000, 9% (v/v) ethylene glycol	Resolution 2.60 Å R-free 0.285
5HZJ Crystal structure of photoinhibitable Intersectin1 containing wildtype LOV2 domain Deposited 2016-02-02	Different construct Different mutation/modification 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 1230–1308（79 aa） Chain A 1309–1580（272 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.5, 9% (w/v) PEG 8000, 9% (v/v) ethylene glycol	Resolution 2.60 Å R-free 0.281
5HZJ Crystal structure of photoinhibitable Intersectin1 containing wildtype LOV2 domain Deposited 2016-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1230–1308（79 aa） Chain B 1309–1580（272 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.5, 9% (w/v) PEG 8000, 9% (v/v) ethylene glycol	Resolution 2.60 Å R-free 0.281
5HZK Crystal structure of photoinhibitable Intersectin1 containing wildtype LOV2 domain in complex with Cdc42 Deposited 2016-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1230–1308（79 aa） Chain B 1309–1580（272 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；0.1 M MES, 20% (w/v) PEG 6000	Resolution 3.30 Å R-free 0.257
5HZK Crystal structure of photoinhibitable Intersectin1 containing wildtype LOV2 domain in complex with Cdc42 Deposited 2016-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1230–1308（79 aa） Chain D 1309–1580（272 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；0.1 M MES, 20% (w/v) PEG 6000	Resolution 3.30 Å R-free 0.257
6GBU Crystal structure of the second SH3 domain of FCHSD2 (SH3-2) in complex with the fourth SH3 domain of ITSN1 (SH3d) Deposited 2018-04-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1069–1133（65 aa） Chain D 1069–1133（65 aa） Chain F 1069–1133（65 aa） Chain H 1069–1133（65 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.5M ammonium sulfate, 10% Glycerol, Tris pH8.5	Resolution 3.44 Å R-free 0.247
6H5T Intersectin SH3A short isoform Deposited 2018-07-25	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 741–835（95 aa）	Not recorded	7PG 2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL × 1 CL CHLORIDE ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；25% (v/v) polyethylene glycol 550 mono-methyl ether, 100 mM MES-NaOH at pH 6.5, and 10 mM ZnSO4	Resolution 1.69 Å R-free 0.191
6H5T Intersectin SH3A short isoform Deposited 2018-07-25	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 741–835（95 aa）	Not recorded	7PG 2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL × 1 ZN ZINC ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；25% (v/v) polyethylene glycol 550 mono-methyl ether, 100 mM MES-NaOH at pH 6.5, and 10 mM ZnSO4	Resolution 1.69 Å R-free 0.191

10 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ITSN1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–121； UniProt 1–111

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	2khn
Deposition date deposition_date	2009-04-09
Structure title title	NMR solution structure of the EH 1 domain from human intersectin-1 protein. Northeast Structural Genomics Consortium target HR3646E.
Keywords keywords	;GFT NMR, high throughput, NESGC, human intersectin-1, Alternative splicing, Calcium, Cell junction, Cell projection, Coiled coil, Endocytosis, Membrane, Phosphoprotein, SH3 domain, Synapse, Synaptosome, SIGNALING PROTEIN, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium ;; SIGNALING PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	19.32 Å
Radius of gyration Rg (electron density) rg_electron	19.12 Å
Forward intensity I(0) i0	1042400000.00
Molecular weight molecular_weight	271930.0 kDa
Excluded volume excluded_volume	339840 Å³
Envelope volume envelope_volume	113680 Å³
Hydration-shell volume shell_volume	31478 Å³
Envelope diameter envelope_diameter	123.7 Å
Shell Rg shell_rg	35.50 Å
Envelope Rg envelope_rg	36.60 Å
Shape Rg shape_rg	19.16 Å
Total Rg total_rg	19.46 Å
Total atoms total_atoms	38060
Residues n_residues	2420
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	52.7 Å
Rg (real space) rg_real	16.54 Å
Rg uncertainty (real space) rg_real_error	0.15 Å
I(0) (real space) i0_real	9.7380e+08
I(0) uncertainty (real space) i0_real_error	1.0000e+07
Rg (reciprocal space) rg_reciprocal	20.34 Å
I(0) (reciprocal space) i0_reciprocal	1042000000.0000
Solution quality estimate total_estimate	0.6143
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.6 Å
Skewness Skewness skewness	0.672
Kurtosis Kurtosis kurtosis	0.265
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	1.1510
Highest regularization parameter α highest_alpha	1073000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.048; Oscil: 0.738; Stabil: 0.992; Sysdev: 0.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2khna1
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.0 — automated matches

Domain ID domain_id	d2khna2
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	2khnA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

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8. Citations (1)

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Description description	Intersectin-1
Molecular weight formula_weight	13614.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	38060

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

fit	/app/data/saxs_computation/kh/2khn/2khn.fit
pddf	/app/data/pr_computation/kh/2khn/2khn.pr.out
profile	/app/data/saxs_computation/kh/2khn/2khn.dat

NMR solution structure of the EH 1 domain from human intersectin-1 protein. Northeast Structural Genomics Consortium target HR3646E.

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

Intersectin-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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)