SAXSdb — 2kr9

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

Kalirin

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 1253–1432	Fragment：DH 1 domain	No other associated polymer	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

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 2KR9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1U3O Solution structure of rat Kalirin N-terminal SH3 domain Deposited 2004-07-22	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1637–1706（70 aa） Fragment：SH3 domain	Not recorded	No recorded non-water small molecule	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
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	KALRN_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–190； UniProt 1253–1432

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	2kr9
Deposition date deposition_date	2009-12-10
Structure title title	Kalirin DH1 NMR structure
Keywords keywords	;Dbl-family GEF, Rho GTPase GEF, Cytoskeleton, Disulfide bond, Guanine-nucleotide releasing factor, Immunoglobulin domain, Kinase, TRANSFERASE ;; TRANSFERASE
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	19.30 Å
Radius of gyration Rg (electron density) rg_electron	18.93 Å
Forward intensity I(0) i0	1429840000.00
Molecular weight molecular_weight	329370.0 kDa
Excluded volume excluded_volume	415280 Å³
Envelope volume envelope_volume	69612 Å³
Hydration-shell volume shell_volume	24048 Å³
Envelope diameter envelope_diameter	85.8 Å
Shell Rg shell_rg	31.26 Å
Envelope Rg envelope_rg	26.21 Å
Shape Rg shape_rg	18.92 Å
Total Rg total_rg	19.22 Å
Total atoms total_atoms	46185
Residues n_residues	2850
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	76.5 Å
Rg (real space) rg_real	19.41 Å
Rg uncertainty (real space) rg_real_error	0.74 Å
I(0) (real space) i0_real	1.4300e+09
I(0) uncertainty (real space) i0_real_error	1.7490e+07
Rg (reciprocal space) rg_reciprocal	19.40 Å
I(0) (reciprocal space) i0_reciprocal	1430000000.0000
Solution quality estimate total_estimate	0.7473
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.4 Å
Skewness Skewness skewness	0.505
Kurtosis Kurtosis kurtosis	-0.077
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1929000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.438; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.405; Smooth: 0.993

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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) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2kr9A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	900 — Dbl Homology Domain; Chain A
Homologous superfamily homologous superfamily	10 — Dbl homology (DH) domain

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8. Citations (1)

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Description description	Kalirin
Molecular weight formula_weight	21995.2 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	46185

来源生物 organism	Rattus norvegicus
通用名 common_name	rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/kr/2kr9/2kr9.fit
pddf	/app/data/pr_computation/kr/2kr9/2kr9.pr.out
profile	/app/data/saxs_computation/kr/2kr9/2kr9.dat

Kalirin DH1 NMR structure

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

Kalirin

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) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)