SAXSdb — 2ckk

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

KIN17

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 268–393	Fragment：C-TERMINAL DOMAIN, RESIDUES 268-393	IOD IODIDE ION × 12 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.3；290 K；VAPOR DIFFUSION, SITTING DROP 10% ETHYLENE GLYCOL, 27% PEG 6000, 500 MM LICL, 100 MM SODIUM ACETATE PH 6.3 290 K	Resolution 1.45 Å R-free 0.175

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 2CKK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2V1N SOLUTION STRUCTURE OF THE REGION 51-160 OF HUMAN KIN17 REVEALS A WINGED HELIX FOLD Deposited 2007-05-27	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 51–160（110 aa） Fragment：RESIDUES 51-160	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 50MM PHOSPHATE , 150MM NACL NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 50MM PHOSPHATE , 150MM NACL NMR sample composition 90%WATER / 10%D2O	Resolution not provided
7ABH Human pre-Bact-2 spliceosome (SF3b/U2 snRNP portion) Deposited 2020-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: hexadecameric	Chain 7 1–393（393 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
7ABI Human pre-Bact-2 spliceosome Deposited 2020-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric	Chain 7 1–393（393 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.00 Å
8I0P The cryo-EM structure of human pre-Bact complex Deposited 2023-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 51-meric	Chain K 1–393（393 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9COJ SH3-like tandem domain of human KIN protein Deposited 2024-07-16	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 268–393（126 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298.4 K；Ionic strength (raw mmCIF value) 50 mM NaPi, 100 mM NaCl；Pressure 1 NMR sample composition 500 uM [U-13C; U-15N] SH3-like tandem domain of human KIN protein, 0.5 mM PMSF, 3 mM EDTA, 0.02 % v/v sodium azide, 0.33 mM 98% 2H DSS, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	O60870_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–127； UniProt 268–393

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	2ckk
Deposition date deposition_date	2006-04-20
Structure title title	High resolution crystal structure of the human kin17 C-terminal domain containing a kow motif
Keywords keywords	BETA BARREL, RIBOSOMAL PROTEIN, RIBONUCLEOPROTEIN, NUCLEAR PROTEIN; NUCLEAR 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	15.68 Å
Radius of gyration Rg (electron density) rg_electron	14.56 Å
Forward intensity I(0) i0	5473240.00
Molecular weight molecular_weight	15053.0 kDa
Excluded volume excluded_volume	17714 Å³
Envelope volume envelope_volume	19772 Å³
Hydration-shell volume shell_volume	11892 Å³
Envelope diameter envelope_diameter	49.6 Å
Shell Rg shell_rg	19.71 Å
Envelope Rg envelope_rg	14.69 Å
Shape Rg shape_rg	14.43 Å
Total Rg total_rg	15.76 Å
Total atoms total_atoms	965
Residues n_residues	120
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	50.1 Å
Rg (real space) rg_real	15.60 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	5.4730e+06
I(0) uncertainty (real space) i0_real_error	5.5910e+04
Rg (reciprocal space) rg_reciprocal	15.61 Å
I(0) (reciprocal space) i0_reciprocal	5473000.0000
Solution quality estimate total_estimate	0.8867
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.7 Å
Skewness Skewness skewness	0.181
Kurtosis Kurtosis kurtosis	-0.316
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	413600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.882; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.879

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	KIN17
Molecular weight formula_weight	14348.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1181

GEEEKKRTARTDYWLQPEIIVKIITKKLGEKYHKKKAIVKEVIDKYTAVVKMIDSGDKLKLDQTHLETVIPAPGKRILVLNGGYRGNEGTLESINEKTFSATIVIETGPLKGRRVEGIQYEDISKLA

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	211

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2ckkA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	2ckkA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

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8. Citations (1)

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Unit-cell length a length_a	45.752 Å
Unit-cell length b length_b	46.309 Å
Unit-cell length c length_c	60.798 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	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	32.620 Å
R factor r_factor	0.1390
R_work r_work	0.1370
R_free r_free	0.1750

fit	/app/data/saxs_computation/ck/2ckk/2ckk.fit
pddf	/app/data/pr_computation/ck/2ckk/2ckk.pr.out
profile	/app/data/saxs_computation/ck/2ckk/2ckk.dat

High resolution crystal structure of the human kin17 C-terminal domain containing a kow motif

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

KIN17

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