SAXSdb — 1u3o

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

Huntingtin-associated protein-interacting protein

Rattus norvegicus

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 1637–1706	Fragment：SH3 domain	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.4；298 K；Ionic strength (raw mmCIF value) 200 mM；Pressure ambient NMR sample composition：0.4 mM U-15N protein, 50 mM HEPES, 150 mM NaCl, 1 mM dithiotheitol, 92.5% H2O, 7.5% D2O \| 92.5% H2O, 7.5% D2O NMR sample composition：1 mM U-15N,13C protein, 50 mM HEPES, 150 mM NaCl, 1 mM dithiotheitol, 92.5% H2O, 7.5% D2O \| 92.5% H2O, 7.5% 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 1U3O	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2KR9 Kalirin DH1 NMR structure Deposited 2009-12-10	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1253–1432（180 aa） Fragment：DH 1 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298.15 K；Ionic strength (raw mmCIF value) 0.05；Pressure 1.00 NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] KalDH1, 50.0 mM Hepes, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.56 mM [U-100% 15N] KalDH1, 50.00 mM Hepes, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5O33 A structure of the GEF Kalirin DH1 domain in complex with the small GTPase Rac1 Deposited 2017-05-23	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 1253–1432（180 aa） Fragment：UNP residues 1253-1432	Not recorded	EDO 1,2-ETHANEDIOL × 6 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；293 K；0.1M citrate pH4.2, 0.2M sodium chloride, 18% (W/V) PEG 8000	Resolution 1.64 Å R-free 0.240
9HU8 Crystal structure of Kalirin/Rac1 in complex with MC-278. Deposited 2024-12-20	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 1253–1432（180 aa）	Not recorded	A1IXV 2-chloranyl-~{N}-(2-oxidanylidene-5,6,7,8-tetrahydro-1~{H}-1,8-naphthyridin-4-yl)ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M citrate pH 4.2, 0.2 M NaCl and 18 % PEG 8K	Resolution 1.48 Å R-free 0.231
9I1L Crystal structure of Kalirin/Rac1 in complex with RS-009 Deposited 2025-01-16	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 1253–1432（180 aa） Fragment：UNP residues 1253-1432	Not recorded	A1IZQ 2-chloranyl-~{N}-(6-oxidanylidene-1,7-dihydropyrrolo[2,3-b]pyridin-4-yl)ethanamide × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M bis-tris pH 5.5, 0.1 M NaCl, 27% PEG 3350	Resolution 1.68 Å R-free 0.269
9IFK Crystal structure of Kalirin/Rac1 in complex with DK-2 Deposited 2025-02-18	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 1253–1432（180 aa） Fragment：UNP residues 1253-1432	Not recorded	A1I32 2-chloranyl-~{N}-(2-oxidanylidene-1~{H}-quinolin-4-yl)ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M citrate pH 4.7, 0.8 M LiCl and 25% PEG 6K.	Resolution 1.34 Å R-free 0.235
9IG1 Crystal structure of Kalirin/Rac1 in complex with DK-652 Deposited 2025-02-18	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 1253–1432（180 aa） Fragment：UNP residues 1253-1432	Not recorded	A1I33 2-chloranyl-~{N}-(1-oxidanylidene-2~{H}-isoquinolin-7-yl)ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M bis-tris pH 5.5, 0.2 M NaCl and 25% PEG 3350	Resolution 1.65 Å R-free 0.293

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HAPIP_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–82； UniProt 1637–1706

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	1u3o
Deposition date deposition_date	2004-07-22
Structure title title	Solution structure of rat Kalirin N-terminal SH3 domain
Keywords keywords	SH3, cis-Proline, signaling protein; 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	11.37 Å
Radius of gyration Rg (electron density) rg_electron	11.00 Å
Forward intensity I(0) i0	321311000.00
Molecular weight molecular_weight	143460.0 kDa
Excluded volume excluded_volume	176530 Å³
Envelope volume envelope_volume	16344 Å³
Hydration-shell volume shell_volume	10778 Å³
Envelope diameter envelope_diameter	42.7 Å
Shell Rg shell_rg	18.58 Å
Envelope Rg envelope_rg	13.43 Å
Shape Rg shape_rg	11.00 Å
Total Rg total_rg	11.18 Å
Total atoms total_atoms	19920
Residues n_residues	1340
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	37.6 Å
Rg (real space) rg_real	11.30 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	3.2130e+08
I(0) uncertainty (real space) i0_real_error	3.1230e+06
Rg (reciprocal space) rg_reciprocal	11.30 Å
I(0) (reciprocal space) i0_reciprocal	321300000.0000
Solution quality estimate total_estimate	0.8657
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.2 Å
Skewness Skewness skewness	0.117
Kurtosis Kurtosis kurtosis	-0.208
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	105800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.757; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.979

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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1u3oa_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	1u3oA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

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8. Citations (1)

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Description description	Huntingtin-associated protein-interacting protein
Molecular weight formula_weight	8578.6 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	19920

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

fit	/app/data/saxs_computation/u3/1u3o/1u3o.fit
pddf	/app/data/pr_computation/u3/1u3o/1u3o.pr.out
profile	/app/data/saxs_computation/u3/1u3o/1u3o.dat

Solution structure of rat Kalirin N-terminal SH3 domain

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

Huntingtin-associated protein-interacting protein

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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)