SAXSdb — 5l1m

▼

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

Caskin-2

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 483–633	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；278 K；0.1 M Tris pH 7.5, 2.4 M sodium formate, 5 mM DTT	Resolution 2.75 Å R-free 0.265

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 5L1M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2KE9 NMR solution structure of the CASKIN SH3 domain Deposited 2009-01-27	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 284–348（65 aa） Fragment：SH3 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.8；293 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR sample composition 0.6 mM [U-98% 13C; U-98% 15N] caskinSH3-1, 10 mM D2O-2, 0.05 % sodium azide-3, 150 mM sodium chloride-4, 20 mM sodium phosphate-5, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
4IS7 Crystal Structure of the CASKIN2 SAM Domain Tandem Deposited 2013-01-16	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 483–633（151 aa） Fragment：UNP residues 483-633	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2.4 M NaF, 15% glycerol, 0.1 M Tris-HCl, 0.5 mM protein, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.75 Å R-free 0.267
7ZW4 Crystal structure of Talin R7R8 domains with Caskin-2 LD-peptide Deposited 2022-05-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1178–1202（25 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M bis-Tris propane pH 7.0, 0.1 M NaBr and 24% PEG3350	Resolution 2.72 Å R-free 0.269

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CSKI2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 34–184； UniProt 483–633

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5l1m
Deposition date deposition_date	2016-07-29
Structure title title	CASKIN2 SAM domain tandem
Keywords keywords	signaling protein, protein interaction domain, sterile alpha motif, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	21.19 Å
Radius of gyration Rg (electron density) rg_electron	20.71 Å
Forward intensity I(0) i0	4254850.00
Molecular weight molecular_weight	15590.0 kDa
Excluded volume excluded_volume	19744 Å³
Envelope volume envelope_volume	24989 Å³
Hydration-shell volume shell_volume	11253 Å³
Envelope diameter envelope_diameter	69.0 Å
Shell Rg shell_rg	24.39 Å
Envelope Rg envelope_rg	20.49 Å
Shape Rg shape_rg	20.70 Å
Total Rg total_rg	21.35 Å
Total atoms total_atoms	1100
Residues n_residues	140
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	67.7 Å
Rg (real space) rg_real	21.39 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	4.2550e+06
I(0) uncertainty (real space) i0_real_error	6.2990e+04
Rg (reciprocal space) rg_reciprocal	21.36 Å
I(0) (reciprocal space) i0_reciprocal	4255000.0000
Solution quality estimate total_estimate	0.7577
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.9 Å
Skewness Skewness skewness	0.362
Kurtosis Kurtosis kurtosis	-0.848
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1122000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.427; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.584; Smooth: 0.982

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5l1ma1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d5l1ma2
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	5l1mA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	50 — Transcription Factor, Ets-1

Domain ID domain_id	5l1mA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	50 — Transcription Factor, Ets-1

▶

8. Citations (1)

▶

Unit-cell length a length_a	96.460 Å
Unit-cell length b length_b	96.460 Å
Unit-cell length c length_c	119.170 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	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.751 Å
Low-resolution limit resolution_low	48.509 Å
R factor r_factor	0.2471
R_work r_work	0.2449
R_free r_free	0.2649

Description description	Caskin-2
Molecular weight formula_weight	20307.1 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	1100

CASKIN2 SAM domain tandem

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

Caskin-2

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

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

fit	/app/data/saxs_computation/l1/5l1m/5l1m.fit
pddf	/app/data/pr_computation/l1/5l1m/5l1m.pr.out
profile	/app/data/saxs_computation/l1/5l1m/5l1m.dat