SAXSdb — 1kdk

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

Sex Hormone-Binding Globulin

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 1–170	Fragment：N-terminal LG-domain	DHT 5-ALPHA-DIHYDROTESTOSTERONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG400, Isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.245

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 1KDK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D2S CRYSTAL STRUCTURE OF THE N-TERMINAL LAMININ G-LIKE DOMAIN OF SHBG IN COMPLEX WITH DIHYDROTESTOSTERONE Deposited 1999-09-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–211（182 aa） Fragment：RESIDUES 1 TO 205	Not recorded	CA CALCIUM ION × 4 DHT 5-ALPHA-DIHYDROTESTOSTERONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG400, HEPES, CALCIUM CHLORIDE, DIHYDROTESTOSTERONE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K	Resolution 1.55 Å R-free 0.251
1F5F CRYSTAL STRUCTURE OF THE N-TERMINAL G-DOMAIN OF SHBG IN COMPLEX WITH ZINC Deposited 2000-06-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–234（205 aa） Fragment：N-TERMINAL FRAGMENT OF SHBG (RESIDUES 1 TO 205)	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 4 DHT 5-ALPHA-DIHYDROTESTOSTERONE × 2 IPA ISOPROPYL ALCOHOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；Crystal growth: ISOPROPANOL, PEG400, HEPES-buffer, CaCl2, DHT Crystals were soaked with 2.5 mM ZnCl2 for three days, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.70 Å R-free 0.259
1KDM THE CRYSTAL STRUCTURE OF THE HUMAN SEX HORMONE-BINDING GLOBULIN (TETRAGONAL CRYSTAL FORM) Deposited 2001-11-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–170（170 aa） Fragment：N-terminal LG-domain	Not recorded	CA CALCIUM ION × 2 DHT 5-ALPHA-DIHYDROTESTOSTERONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG4000, isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.35 Å R-free 0.264
1LHN CRYSTAL STRUCTURE OF THE N-TERMINAL LG-DOMAIN OF SHBG IN COMPLEX WITH 5ALPHA-ANDROSTANE-3BETA,17ALPHA-DIOL Deposited 2002-04-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–218（189 aa） Fragment：LG-like 1 domain, Residues 30-218	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2 AON 5-ALPHA-ANDROSTANE-3-BETA,17-ALPHA-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Hepes, Calcium chloride, 17a-DHA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.239
1LHO CRYSTAL STRUCTURE OF THE N-TERMINAL LG-DOMAIN OF SHBG IN COMPLEX WITH 5ALPHA-ANDROSTANE-3BETA,17BETA-DIOL Deposited 2002-04-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–218（189 aa） Fragment：LG-like 1 domain, Residues 30-218	Not recorded	CA CALCIUM ION × 2 AOM 5-ALPHA-ANDROSTANE-3-BETA,17BETA-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；HEPES, Calcium chloride, 17b-DHA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.223
1LHU CRYSTAL STRUCTURE OF THE N-TERMINAL LG-DOMAIN OF SHBG IN COMPLEX WITH ESTRADIOL Deposited 2002-04-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–218（189 aa） Fragment：LG-like 1 domain, Residues 43-218	Not recorded	CA CALCIUM ION × 2 EST ESTRADIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；HEPES, Calcium chloride, estradiol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.237
1LHV CRYSTAL STRUCTURE OF THE N-TERMINAL LG-DOMAIN OF SHBG IN COMPLEX WITH NORGESTREL Deposited 2002-04-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–218（189 aa） Fragment：LG-like 1 domain, Residues 30-218	Not recorded	CA CALCIUM ION × 2 ZN ZINC ION × 2 NOG 13-BETA-ETHYL-17-ALPHA-ETHYNYL-17-BETA-HYDROXYGON-4-EN-3-ONE × 2 IPA ISOPROPYL ALCOHOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；HEPES, Calcium chloride, norgestrel, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.264
1LHW CRYSTAL STRUCTURE OF THE N-TERMINAL LG-DOMAIN OF SHBG IN COMPLEX WITH 2-METHOXYESTRADIOL Deposited 2002-04-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–218（189 aa） Fragment：LG-like 1 domain, Residues 30-218	Not recorded	CA CALCIUM ION × 2 ESM 1,3,5(10)-ESTRATRIEN-2,3,17-BETA-TRIOL 2-METHYL ETHER × 2 IPA ISOPROPYL ALCOHOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；HEPES, Calcium chloride, 2-methoxyestradiol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.75 Å R-free 0.238
6PYA Sex Hormone-binding globulin mutant E176K in complex with IPI Deposited 2019-07-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–234（205 aa）	Mutation：E176K	P57 3-[(1H-imidazol-1-yl)methyl]-2-phenyl-1H-indole × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；20% Peg 3350, 0.2 M potassium thiocyanate, HEPES pH 7.5, 2.5 mM Calcium Chloride	Resolution 1.71 Å R-free 0.216
6PYB Sex Hormone-binding globulin mutant E176K in complex with DVT Deposited 2019-07-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–234（205 aa）	Mutation：E176K	P5G 4,4'-[(3R,4R)-oxolane-3,4-diylbis(methylene)]bis(2-methoxyphenol) × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；PEG 3350, Potassium thiocyanate	Resolution 1.80 Å R-free 0.231
6PYF Sex Hormone-binding globulin mutant E176K in complex with Estradiol Deposited 2019-07-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–234（205 aa）	Mutation：E176K	CA CALCIUM ION × 2 EST ESTRADIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；PEG 3350, potassium thiocyanate	Resolution 1.73 Å R-free 0.220
6ULB Sex Hormone-binding globulin mutant E176K in complex with Danazol Deposited 2019-10-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–234（205 aa）	Mutation：E176K	CA CALCIUM ION × 2 QA1 Danazol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；20% PEG 3350, 0.2M potassium thiocyanate	Resolution 1.75 Å R-free 0.225

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

View Construct and Data Evidence

UniProt name	SHBG_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–177； UniProt 1–170

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	1kdk
Deposition date deposition_date	2001-11-13
Structure title title	THE STRUCTURE OF THE N-TERMINAL LG DOMAIN OF SHBG IN CRYSTALS SOAKED WITH EDTA
Keywords keywords	SHBG, DHT, TRANSPORT PROTEIN; TRANSPORT 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	16.66 Å
Radius of gyration Rg (electron density) rg_electron	15.11 Å
Forward intensity I(0) i0	7310660.00
Molecular weight molecular_weight	19856.0 kDa
Excluded volume excluded_volume	24908 Å³
Envelope volume envelope_volume	27451 Å³
Hydration-shell volume shell_volume	15070 Å³
Envelope diameter envelope_diameter	48.6 Å
Shell Rg shell_rg	21.29 Å
Envelope Rg envelope_rg	15.29 Å
Shape Rg shape_rg	15.10 Å
Total Rg total_rg	16.21 Å
Total atoms total_atoms	1399
Residues n_residues	177
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	49.6 Å
Rg (real space) rg_real	16.52 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	7.3110e+06
I(0) uncertainty (real space) i0_real_error	9.1340e+04
Rg (reciprocal space) rg_reciprocal	16.54 Å
I(0) (reciprocal space) i0_reciprocal	7311000.0000
Solution quality estimate total_estimate	0.7495
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.5 Å
Skewness Skewness skewness	0.004
Kurtosis Kurtosis kurtosis	-0.489
Angular range angular_range	— – 0.4800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1345000.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 0.338; Positv: 1.000; Valcen: 0.971; Smooth: 0.967

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Sex Hormone-Binding Globulin
Molecular weight formula_weight	19655.3 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	1499

DPPAVHLSNGPGQEPIAVMTFDLTKITKTSSSFEVRTWDPEGVIFYGDTNPKDDWFMLGLRDGRPEIQLHNHWAQLTVGAGPRLDDGRWHQVEVKMEGDSVLLEVDGEEVLRLRQVSGPLTSKRHPIMRIALGGLLFPASNLRLPLVPALDGCLRRDSWLDKQAEISASAPTSLRSC

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	5-ALPHA-DIHYDROTESTOSTERONE
Molecular weight formula_weight	290.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	89

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1kdka_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.4 — Laminin G-like module

CATH v4.4 (1 domains)

Domain ID domain_id	1kdkA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

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8. Citations (1)

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Unit-cell length a length_a	103.720 Å
Unit-cell length b length_b	103.720 Å
Unit-cell length c length_c	85.760 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	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1940
R_free r_free	0.2450

fit	/app/data/saxs_computation/kd/1kdk/1kdk.fit
pddf	/app/data/pr_computation/kd/1kdk/1kdk.pr.out
profile	/app/data/saxs_computation/kd/1kdk/1kdk.dat

THE STRUCTURE OF THE N-TERMINAL LG DOMAIN OF SHBG IN CRYSTALS SOAKED WITH EDTA

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

Sex Hormone-Binding Globulin

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