3eq5

Crystal structure of fragment 137 to 238 of the human Ski-like protein

Method: X-RAY DIFFRACTION D_max: 115.6 Å Quality: GOOD

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

Ski-like protein

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 137–238	Fragment：UNP Residues 137-238	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG 3350, 0.2M Ammonium nitrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.45 Å R-free 0.274
10	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain J； UniProt 137–238	Fragment：UNP Residues 137-238	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG 3350, 0.2M Ammonium nitrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.45 Å R-free 0.274
11	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain K； UniProt 137–238	Fragment：UNP Residues 137-238	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG 3350, 0.2M Ammonium nitrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.45 Å R-free 0.274
12	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain L； UniProt 137–238	Fragment：UNP Residues 137-238	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG 3350, 0.2M Ammonium nitrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.45 Å R-free 0.274
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 137–238	Fragment：UNP Residues 137-238	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG 3350, 0.2M Ammonium nitrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.45 Å R-free 0.274
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 137–238	Fragment：UNP Residues 137-238	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG 3350, 0.2M Ammonium nitrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.45 Å R-free 0.274
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 137–238	Fragment：UNP Residues 137-238	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG 3350, 0.2M Ammonium nitrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.45 Å R-free 0.274
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 137–238	Fragment：UNP Residues 137-238	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG 3350, 0.2M Ammonium nitrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.45 Å R-free 0.274
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 137–238	Fragment：UNP Residues 137-238	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG 3350, 0.2M Ammonium nitrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.45 Å R-free 0.274
7	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain G； UniProt 137–238	Fragment：UNP Residues 137-238	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG 3350, 0.2M Ammonium nitrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.45 Å R-free 0.274
8	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain H； UniProt 137–238	Fragment：UNP Residues 137-238	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG 3350, 0.2M Ammonium nitrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.45 Å R-free 0.274
9	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain I； UniProt 137–238	Fragment：UNP Residues 137-238	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG 3350, 0.2M Ammonium nitrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.45 Å R-free 0.274

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 3EQ5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5C4V Ski-like protein Deposited 2015-06-18	Different construct 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 238–356（119 aa） Fragment：residues 238-356	Not recorded	GOL GLYCEROL × 1 ZN ZINC ION × 1 NI NICKEL (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；2.8-3.3 M sodium chloride, 0.1 M Bis-Tris pH 5.5	Resolution 2.60 Å R-free 0.242
5C4V Ski-like protein Deposited 2015-06-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 238–356（119 aa） Fragment：residues 238-356	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；2.8-3.3 M sodium chloride, 0.1 M Bis-Tris pH 5.5	Resolution 2.60 Å R-free 0.242
5C4V Ski-like protein Deposited 2015-06-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 238–356（119 aa） Fragment：residues 238-356	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；2.8-3.3 M sodium chloride, 0.1 M Bis-Tris pH 5.5	Resolution 2.60 Å R-free 0.242

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

View Construct and Data Evidence

UniProt name	SKIL_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–125； UniProt 137–238 Author chain B； PDBConstruct 24–125； UniProt 137–238 Author chain C； PDBConstruct 24–125； UniProt 137–238 Author chain D； PDBConstruct 24–125； UniProt 137–238 Author chain E； PDBConstruct 24–125； UniProt 137–238 Author chain F； PDBConstruct 24–125； UniProt 137–238 Author chain G； PDBConstruct 24–125； UniProt 137–238 Author chain H； PDBConstruct 24–125； UniProt 137–238 Author chain I； PDBConstruct 24–125； UniProt 137–238 Author chain J； PDBConstruct 24–125； UniProt 137–238 Author chain K； PDBConstruct 24–125； UniProt 137–238 Author chain L； PDBConstruct 24–125； UniProt 137–238

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3eq5
Deposition date deposition_date	2008-09-30
Structure title title	Crystal structure of fragment 137 to 238 of the human Ski-like protein
Keywords keywords	;SKIL, SKI-LIKE PROTEIN, SNO, RECEPTOR SIGNALLING, TGF-BETA, SIGNALING PROTEIN, Structural Genomics, SGC Stockholm, Structural Genomics Consortium, SGC ;; 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	36.72 Å
Radius of gyration Rg (electron density) rg_electron	36.12 Å
Forward intensity I(0) i0	255860000.00
Molecular weight molecular_weight	128610.0 kDa
Excluded volume excluded_volume	161500 Å³
Envelope volume envelope_volume	229870 Å³
Hydration-shell volume shell_volume	53634 Å³
Envelope diameter envelope_diameter	124.4 Å
Shell Rg shell_rg	42.20 Å
Envelope Rg envelope_rg	35.10 Å
Shape Rg shape_rg	36.14 Å
Total Rg total_rg	36.52 Å
Total atoms total_atoms	8968
Residues n_residues	1156
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	115.6 Å
Rg (real space) rg_real	36.54 Å
Rg uncertainty (real space) rg_real_error	0.74 Å
I(0) (real space) i0_real	2.5590e+08
I(0) uncertainty (real space) i0_real_error	3.9590e+06
Rg (reciprocal space) rg_reciprocal	36.65 Å
I(0) (reciprocal space) i0_reciprocal	255900000.0000
Solution quality estimate total_estimate	0.8898
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	45.7 Å
Skewness Skewness skewness	0.175
Kurtosis Kurtosis kurtosis	-0.377
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	19870000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.897

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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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7. Fold Classification (SCOP + CATH) 25 domains

SCOP 2.08 (13 domains)

Domain ID domain_id	d3eq5a1
Class class	a — All alpha proteins
Fold Fold fold	a.6 — Putative DNA-binding domain
Superfamily Superfamily superfamily	a.6.1 — Putative DNA-binding domain
Family Family family	a.6.1.4 — Dachshund-homology domain

Domain ID domain_id	d3eq5a2
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

Domain ID domain_id	d3eq5b_
Class class	a — All alpha proteins
Fold Fold fold	a.6 — Putative DNA-binding domain
Superfamily Superfamily superfamily	a.6.1 — Putative DNA-binding domain
Family Family family	a.6.1.4 — Dachshund-homology domain

Domain ID domain_id	d3eq5c_
Class class	a — All alpha proteins
Fold Fold fold	a.6 — Putative DNA-binding domain
Superfamily Superfamily superfamily	a.6.1 — Putative DNA-binding domain
Family Family family	a.6.1.4 — Dachshund-homology domain

Domain ID domain_id	d3eq5d_
Class class	a — All alpha proteins
Fold Fold fold	a.6 — Putative DNA-binding domain
Superfamily Superfamily superfamily	a.6.1 — Putative DNA-binding domain
Family Family family	a.6.1.4 — Dachshund-homology domain

Domain ID domain_id	d3eq5e_
Class class	a — All alpha proteins
Fold Fold fold	a.6 — Putative DNA-binding domain
Superfamily Superfamily superfamily	a.6.1 — Putative DNA-binding domain
Family Family family	a.6.1.4 — Dachshund-homology domain

Domain ID domain_id	d3eq5f_
Class class	a — All alpha proteins
Fold Fold fold	a.6 — Putative DNA-binding domain
Superfamily Superfamily superfamily	a.6.1 — Putative DNA-binding domain
Family Family family	a.6.1.4 — Dachshund-homology domain

Domain ID domain_id	d3eq5g_
Class class	a — All alpha proteins
Fold Fold fold	a.6 — Putative DNA-binding domain
Superfamily Superfamily superfamily	a.6.1 — Putative DNA-binding domain
Family Family family	a.6.1.4 — Dachshund-homology domain

Domain ID domain_id	d3eq5h_
Class class	a — All alpha proteins
Fold Fold fold	a.6 — Putative DNA-binding domain
Superfamily Superfamily superfamily	a.6.1 — Putative DNA-binding domain
Family Family family	a.6.1.4 — Dachshund-homology domain

Domain ID domain_id	d3eq5i_
Class class	a — All alpha proteins
Fold Fold fold	a.6 — Putative DNA-binding domain
Superfamily Superfamily superfamily	a.6.1 — Putative DNA-binding domain
Family Family family	a.6.1.4 — Dachshund-homology domain

Domain ID domain_id	d3eq5j_
Class class	a — All alpha proteins
Fold Fold fold	a.6 — Putative DNA-binding domain
Superfamily Superfamily superfamily	a.6.1 — Putative DNA-binding domain
Family Family family	a.6.1.4 — Dachshund-homology domain

Domain ID domain_id	d3eq5k_
Class class	a — All alpha proteins
Fold Fold fold	a.6 — Putative DNA-binding domain
Superfamily Superfamily superfamily	a.6.1 — Putative DNA-binding domain
Family Family family	a.6.1.4 — Dachshund-homology domain

Domain ID domain_id	d3eq5l_
Class class	a — All alpha proteins
Fold Fold fold	a.6 — Putative DNA-binding domain
Superfamily Superfamily superfamily	a.6.1 — Putative DNA-binding domain
Family Family family	a.6.1.4 — Dachshund-homology domain

CATH v4.4 (12 domains)

Domain ID domain_id	3eq5A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	260 — Mlu1-box Binding Protein; DNA-binding Domain
Homologous superfamily homologous superfamily	20 — Ski

Domain ID domain_id	3eq5B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	260 — Mlu1-box Binding Protein; DNA-binding Domain
Homologous superfamily homologous superfamily	20 — Ski

Domain ID domain_id	3eq5C00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	260 — Mlu1-box Binding Protein; DNA-binding Domain
Homologous superfamily homologous superfamily	20 — Ski

Domain ID domain_id	3eq5D00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	260 — Mlu1-box Binding Protein; DNA-binding Domain
Homologous superfamily homologous superfamily	20 — Ski

Domain ID domain_id	3eq5E00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	260 — Mlu1-box Binding Protein; DNA-binding Domain
Homologous superfamily homologous superfamily	20 — Ski

Domain ID domain_id	3eq5F00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	260 — Mlu1-box Binding Protein; DNA-binding Domain
Homologous superfamily homologous superfamily	20 — Ski

Domain ID domain_id	3eq5G00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	260 — Mlu1-box Binding Protein; DNA-binding Domain
Homologous superfamily homologous superfamily	20 — Ski

Domain ID domain_id	3eq5H00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	260 — Mlu1-box Binding Protein; DNA-binding Domain
Homologous superfamily homologous superfamily	20 — Ski

Domain ID domain_id	3eq5I00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	260 — Mlu1-box Binding Protein; DNA-binding Domain
Homologous superfamily homologous superfamily	20 — Ski

Domain ID domain_id	3eq5J00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	260 — Mlu1-box Binding Protein; DNA-binding Domain
Homologous superfamily homologous superfamily	20 — Ski

Domain ID domain_id	3eq5K00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	260 — Mlu1-box Binding Protein; DNA-binding Domain
Homologous superfamily homologous superfamily	20 — Ski

Domain ID domain_id	3eq5L00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	260 — Mlu1-box Binding Protein; DNA-binding Domain
Homologous superfamily homologous superfamily	20 — Ski

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8. Citations (1)

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Unit-cell length a length_a	210.820 Å
Unit-cell length b length_b	70.120 Å
Unit-cell length c length_c	116.280 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.95 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	19.830 Å
R factor r_factor	0.2345
R_work r_work	0.2324
R_free r_free	0.2743

Description description	Ski-like protein
Molecular weight formula_weight	14001.0 kDa
Source method src_method	man
Copy count entity_count	12

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	9437

Crystal structure of fragment 137 to 238 of the human Ski-like protein

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

Ski-like 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

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

7. Fold Classification (SCOP + CATH) 25 domains

SCOP 2.08 (13 domains)

CATH v4.4 (12 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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	343

fit	/app/data/saxs_computation/eq/3eq5/3eq5.fit
pddf	/app/data/pr_computation/eq/3eq5/3eq5.pr.out
profile	/app/data/saxs_computation/eq/3eq5/3eq5.dat