SAXSdb — 1lhv

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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 30–218	Fragment：LG-like 1 domain, Residues 30-218	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

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 1LHV	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
1KDK THE STRUCTURE OF THE N-TERMINAL LG DOMAIN OF SHBG IN CRYSTALS SOAKED WITH EDTA Deposited 2001-11-13	Different construct 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	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
1KDM THE CRYSTAL STRUCTURE OF THE HUMAN SEX HORMONE-BINDING GLOBULIN (TETRAGONAL CRYSTAL FORM) Deposited 2001-11-13	Different construct 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 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 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
1LHW CRYSTAL STRUCTURE OF THE N-TERMINAL LG-DOMAIN OF SHBG IN COMPLEX WITH 2-METHOXYESTRADIOL Deposited 2002-04-17	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 1–189； UniProt 30–218

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	1lhv
Deposition date deposition_date	2002-04-17
Structure title title	CRYSTAL STRUCTURE OF THE N-TERMINAL LG-DOMAIN OF SHBG IN COMPLEX WITH NORGESTREL
Keywords keywords	SHBG, Norgestrel, 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	16.61 Å
Radius of gyration Rg (electron density) rg_electron	15.01 Å
Forward intensity I(0) i0	7179720.00
Molecular weight molecular_weight	19586.0 kDa
Excluded volume excluded_volume	24548 Å³
Envelope volume envelope_volume	27002 Å³
Hydration-shell volume shell_volume	14916 Å³
Envelope diameter envelope_diameter	49.6 Å
Shell Rg shell_rg	21.26 Å
Envelope Rg envelope_rg	15.22 Å
Shape Rg shape_rg	15.00 Å
Total Rg total_rg	16.18 Å
Total atoms total_atoms	1375
Residues n_residues	173
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	50.2 Å
Rg (real space) rg_real	16.44 Å
Rg uncertainty (real space) rg_real_error	0.21 Å
I(0) (real space) i0_real	7.1800e+06
I(0) uncertainty (real space) i0_real_error	7.0410e+04
Rg (reciprocal space) rg_reciprocal	16.46 Å
I(0) (reciprocal space) i0_reciprocal	7180000.0000
Solution quality estimate total_estimate	0.8996
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.2 Å
Skewness Skewness skewness	-0.005
Kurtosis Kurtosis kurtosis	-0.482
Angular range angular_range	— – 0.4800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1173000.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 1.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	SEX HORMONE-BINDING GLOBULIN
Molecular weight formula_weight	20972.8 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	1464

LRPVLPTQSAHDPPAVHLSNGPGQEPIAVMTFDLTKITKTSSSFEVRTWDPEGVIFYGDTNPKDDWFMLGLRDGRPEIQLHNHWAQLTVGAGPRLDDGRWHQVEVKMEGDSVLLEVDGEEVLRLRQVSGPLTSKRHPIMRIALGGLLFPASNLRLPLVPALDGCLRRDSWLDKQAEISASAPTSLRSCD

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	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	13-BETA-ETHYL-17-ALPHA-ETHYNYL-17-BETA-HYDROXYGON-4-EN-3-ONE
Molecular weight formula_weight	312.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	64

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1lhva_
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	1lhvA00
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	103.980 Å
Unit-cell length b length_b	103.980 Å
Unit-cell length c length_c	83.930 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	2.000 Å
Low-resolution limit resolution_low	19.650 Å
R factor r_factor	—
R_work r_work	0.2150
R_free r_free	0.2640

fit	/app/data/saxs_computation/lh/1lhv/1lhv.fit
pddf	/app/data/pr_computation/lh/1lhv/1lhv.pr.out
profile	/app/data/saxs_computation/lh/1lhv/1lhv.dat

CRYSTAL STRUCTURE OF THE N-TERMINAL LG-DOMAIN OF SHBG IN COMPLEX WITH NORGESTREL