SAXSdb — 8c7d

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

Kalirin

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 1916–2114	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；20% W/V PEG3350, 0.1 M succinic acid	Resolution 1.86 Å R-free 0.275

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 8C7D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5QQD PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with Z56880342 Deposited 2019-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1280–1459（180 aa）	Mutation：None	EDO 1,2-ETHANEDIOL × 1 JGA N-ethyl-N'-(5-methyl-1,2-oxazol-3-yl)urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1M bis-tris pH 5.5 24% PEG 3350	Resolution 1.91 Å R-free 0.259
5QQE PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-009-531-494 Deposited 2019-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1280–1459（180 aa）	Mutation：None	EDO 1,2-ETHANEDIOL × 1 N5S N-(5-methyl-1,2-oxazol-3-yl)-N'-[(3S)-4,4,4-trifluoro-3-hydroxy-3-(5-methylfuran-2-yl)butyl]urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1M bis-tris pH 5.5 24% PEG 3350	Resolution 1.95 Å R-free 0.284
5QQF PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-004-412-710 Deposited 2019-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1280–1459（180 aa）	Mutation：None	EDO 1,2-ETHANEDIOL × 1 N5V N-ethyl-N'-1,3-thiazol-2-ylurea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1M bis-tris pH 5.5 24% PEG 3350	Resolution 2.26 Å R-free 0.270
5QQG PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-009-541-216 Deposited 2019-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1280–1459（180 aa）	Mutation：None	EDO 1,2-ETHANEDIOL × 1 N64 N-(5-methyl-1,2-oxazol-3-yl)-N'-[3-(4-phenylpiperazin-1-yl)propyl]urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1M bis-tris pH 5.5 24% PEG 3350	Resolution 2.23 Å R-free 0.274
5QQH PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-020-096-465 Deposited 2019-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1280–1459（180 aa）	Mutation：None	EDO 1,2-ETHANEDIOL × 1 N67 N-methyl-5-({[(5-methyl-1,2-oxazol-3-yl)carbamoyl]amino}methyl)thiophene-2-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1M bis-tris pH 5.5 24% PEG 3350	Resolution 2.09 Å R-free 0.263
5QQI PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-009-178-994 Deposited 2019-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1280–1459（180 aa）	Mutation：None	EDO 1,2-ETHANEDIOL × 1 N6D N-[3-(methoxymethyl)phenyl]-N'-(5-methyl-1,2-oxazol-3-yl)urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1M bis-tris pH 5.5 24% PEG 3350	Resolution 2.08 Å R-free 0.277
5QQJ PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-009-587-558 Deposited 2019-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1280–1459（180 aa）	Mutation：None	EDO 1,2-ETHANEDIOL × 1 N6J N-{1-[(imidazo[1,2-a]pyridin-2-yl)methyl]-1H-pyrazol-4-yl}-N'-(5-methyl-1,2-oxazol-3-yl)urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1M bis-tris pH 5.5 24% PEG 3350	Resolution 1.90 Å R-free 0.269
5QQK PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-009-359-835 Deposited 2019-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1280–1459（180 aa）	Mutation：None	EDO 1,2-ETHANEDIOL × 1 N6V N-{1-[2-(diethylamino)ethyl]-1H-indol-5-yl}-N'-(5-methyl-1,2-oxazol-3-yl)urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1M bis-tris pH 5.5 24% PEG 3350	Resolution 2.24 Å R-free 0.266
5QQL PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-009-565-301 Deposited 2019-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1280–1459（180 aa）	Mutation：None	EDO 1,2-ETHANEDIOL × 1 N71 N-(5-methyl-1,2-oxazol-3-yl)-N'-[2-(phenylsulfonyl)ethyl]urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1M bis-tris pH 5.5 24% PEG 3350	Resolution 2.25 Å R-free 0.270
5QQM PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-009-565-325 Deposited 2019-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1280–1459（180 aa）	Mutation：None	EDO 1,2-ETHANEDIOL × 1 N74 N-(1-benzyl-1H-pyrazol-4-yl)-N'-(5-methyl-1,2-oxazol-3-yl)urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1M bis-tris pH 5.5 24% PEG 3350	Resolution 2.02 Å R-free 0.273
5QQN PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-010-382-606 Deposited 2019-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1280–1459（180 aa）	Mutation：None	EDO 1,2-ETHANEDIOL × 1 N5D N-cyclopropyl-2-(4-{[(5-methyl-1,2-oxazol-3-yl)carbamoyl]amino}-1H-pyrazol-1-yl)acetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1M bis-tris pH 5.5 24% PEG 3350	Resolution 2.26 Å R-free 0.279
5QU9 PanDDA analysis group deposition of ground-state model of Kalirin/Rac1 screened against a customized urea fragment library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 Deposited 2019-12-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1280–1459（180 aa）	Mutation：None	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1M bis-tris pH 5.5 24% PEG 3350	Resolution 2.00 Å R-free 0.231

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KALRN_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–201； UniProt 1916–2114

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	8c7d
Deposition date deposition_date	2023-01-14
Structure title title	Structure of the GEF Kalirin DH2 Domain
Keywords keywords	GTPase exchange factor, helical bundle, SIGNALING PROTEIN; SIGNALING PROTEIN
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	19.53 Å
Radius of gyration Rg (electron density) rg_electron	18.57 Å
Forward intensity I(0) i0	7990390.00
Molecular weight molecular_weight	21464.0 kDa
Excluded volume excluded_volume	27121 Å³
Envelope volume envelope_volume	31389 Å³
Hydration-shell volume shell_volume	15085 Å³
Envelope diameter envelope_diameter	73.9 Å
Shell Rg shell_rg	23.64 Å
Envelope Rg envelope_rg	19.02 Å
Shape Rg shape_rg	18.57 Å
Total Rg total_rg	19.43 Å
Total atoms total_atoms	1512
Residues n_residues	195
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	73.0 Å
Rg (real space) rg_real	19.64 Å
Rg uncertainty (real space) rg_real_error	0.81 Å
I(0) (real space) i0_real	7.9900e+06
I(0) uncertainty (real space) i0_real_error	1.2190e+05
Rg (reciprocal space) rg_reciprocal	19.62 Å
I(0) (reciprocal space) i0_reciprocal	7990000.0000
Solution quality estimate total_estimate	0.8010
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.5 Å
Skewness Skewness skewness	0.510
Kurtosis Kurtosis kurtosis	-0.095
Angular range angular_range	— – 0.4050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1744000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.590; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.647; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	27.324 Å
Unit-cell length b length_b	74.478 Å
Unit-cell length c length_c	100.121 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.860 Å
Low-resolution limit resolution_low	59.760 Å
R factor r_factor	0.2298
R_work r_work	0.2273
R_free r_free	0.2745

Description description	Kalirin
Molecular weight formula_weight	24059.9 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	1619

Structure of the GEF Kalirin DH2 Domain

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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	72

fit	/app/data/saxs_computation/c7/8c7d/8c7d.fit
pddf	/app/data/pr_computation/c7/8c7d/8c7d.pr.out
profile	/app/data/saxs_computation/c7/8c7d/8c7d.dat