SAXSdb — 1ikt

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

ESTRADIOL 17 BETA-DEHYDROGENASE 4

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 618–736	Fragment：C-terminal domain, Residues 618-736	SO4 SULFATE ION × 2 OXN OXTOXYNOL-10 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；ammonium sulfate, sodium chloride, Triton X-100, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.75 Å R-free 0.214

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 1IKT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1S9C Crystal structure analysis of the 2-enoyl-CoA hydratase 2 domain of human peroxisomal multifunctional enzyme type 2 Deposited 2004-02-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 318–615（298 aa） Fragment：2-enoyl-coenzyme A hydratase 2 domain Chain B 318–615（298 aa） Fragment：2-enoyl-coenzyme A hydratase 2 domain	Mutation：S318M, T319A, I559V, T615L Mutation：S318M, T319A, I559V, T615L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；PEG 10000, HEPES, MnCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.00 Å R-free 0.265
1S9C Crystal structure analysis of the 2-enoyl-CoA hydratase 2 domain of human peroxisomal multifunctional enzyme type 2 Deposited 2004-02-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 318–615（298 aa） Fragment：2-enoyl-coenzyme A hydratase 2 domain Chain D 318–615（298 aa） Fragment：2-enoyl-coenzyme A hydratase 2 domain	Mutation：S318M, T319A, I559V, T615L Mutation：S318M, T319A, I559V, T615L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；PEG 10000, HEPES, MnCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.00 Å R-free 0.265
1S9C Crystal structure analysis of the 2-enoyl-CoA hydratase 2 domain of human peroxisomal multifunctional enzyme type 2 Deposited 2004-02-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 318–615（298 aa） Fragment：2-enoyl-coenzyme A hydratase 2 domain Chain F 318–615（298 aa） Fragment：2-enoyl-coenzyme A hydratase 2 domain	Mutation：S318M, T319A, I559V, T615L Mutation：S318M, T319A, I559V, T615L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；PEG 10000, HEPES, MnCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.00 Å R-free 0.265
1S9C Crystal structure analysis of the 2-enoyl-CoA hydratase 2 domain of human peroxisomal multifunctional enzyme type 2 Deposited 2004-02-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 318–615（298 aa） Fragment：2-enoyl-coenzyme A hydratase 2 domain Chain H 318–615（298 aa） Fragment：2-enoyl-coenzyme A hydratase 2 domain	Mutation：S318M, T319A, I559V, T615L Mutation：S318M, T319A, I559V, T615L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；PEG 10000, HEPES, MnCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.00 Å R-free 0.265
1S9C Crystal structure analysis of the 2-enoyl-CoA hydratase 2 domain of human peroxisomal multifunctional enzyme type 2 Deposited 2004-02-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain I 318–615（298 aa） Fragment：2-enoyl-coenzyme A hydratase 2 domain Chain J 318–615（298 aa） Fragment：2-enoyl-coenzyme A hydratase 2 domain	Mutation：S318M, T319A, I559V, T615L Mutation：S318M, T319A, I559V, T615L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；PEG 10000, HEPES, MnCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.00 Å R-free 0.265
1S9C Crystal structure analysis of the 2-enoyl-CoA hydratase 2 domain of human peroxisomal multifunctional enzyme type 2 Deposited 2004-02-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain K 318–615（298 aa） Fragment：2-enoyl-coenzyme A hydratase 2 domain Chain L 318–615（298 aa） Fragment：2-enoyl-coenzyme A hydratase 2 domain	Mutation：S318M, T319A, I559V, T615L Mutation：S318M, T319A, I559V, T615L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；PEG 10000, HEPES, MnCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.00 Å R-free 0.265
1ZBQ Crystal Structure Of Human 17-Beta-Hydroxysteroid Dehydrogenase Type 4 In Complex With NAD Deposited 2005-04-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–304（304 aa） Fragment：N-terminal SHORT CHAIN DEHYDROGENASE DOMAIN Chain B 1–304（304 aa） Fragment：N-terminal SHORT CHAIN DEHYDROGENASE DOMAIN	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M Lithium Sulphate monohydrate, 0.1M TRIS hydrochloride pH8.5, 30% w/v polyethylene glycol 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.19 Å R-free 0.236
1ZBQ Crystal Structure Of Human 17-Beta-Hydroxysteroid Dehydrogenase Type 4 In Complex With NAD Deposited 2005-04-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–304（304 aa） Fragment：N-terminal SHORT CHAIN DEHYDROGENASE DOMAIN Chain D 1–304（304 aa） Fragment：N-terminal SHORT CHAIN DEHYDROGENASE DOMAIN	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M Lithium Sulphate monohydrate, 0.1M TRIS hydrochloride pH8.5, 30% w/v polyethylene glycol 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.19 Å R-free 0.236
1ZBQ Crystal Structure Of Human 17-Beta-Hydroxysteroid Dehydrogenase Type 4 In Complex With NAD Deposited 2005-04-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–304（304 aa） Fragment：N-terminal SHORT CHAIN DEHYDROGENASE DOMAIN Chain F 1–304（304 aa） Fragment：N-terminal SHORT CHAIN DEHYDROGENASE DOMAIN	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M Lithium Sulphate monohydrate, 0.1M TRIS hydrochloride pH8.5, 30% w/v polyethylene glycol 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.19 Å R-free 0.236
6Z1W Crystal structure of human steroid carrier protein SL (SCP-2L) mutant A100C Deposited 2020-05-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 643–761（119 aa）	Mutation：A100C	OXN OXTOXYNOL-10 × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；2.2 M ammonium sulfate, 0.2 M NaCl and 0.1 M citric acid	Resolution 2.48 Å R-free 0.268
6Z1X Crystal structure of human steroid carrier protein SL (SCP-2L) mutant V83C Deposited 2020-05-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 643–761（119 aa）	Mutation：V83C	OXN OXTOXYNOL-10 × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；2.2 M ammonium sulfate, 0.2 M NaCl and 0.1 M citric acid	Resolution 2.09 Å R-free 0.237
8AF2 Human Sterol Carrier Protein with unnatural amino acid 2,2'-bipyridine alanine incorporated at position 111 Deposited 2022-07-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 618–736（119 aa）	Mutation：;2,2'-bipyridine alanine incorporated at position 111 ; Non-standard monomer：Yes (specific site not provided by mmCIF)	TRT FRAGMENT OF TRITON X-100 × 2 SO4 SULFATE ION × 1 CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；281 K；well solution 2.3M ammonium sulphate, 100 mM citric acid pH 5.6 and 200 mM NaCl	Resolution 2.51 Å R-free 0.300
8AF2 Human Sterol Carrier Protein with unnatural amino acid 2,2'-bipyridine alanine incorporated at position 111 Deposited 2022-07-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 618–736（119 aa）	Mutation：;2,2'-bipyridine alanine incorporated at position 111 ; Non-standard monomer：Yes (specific site not provided by mmCIF)	TRT FRAGMENT OF TRITON X-100 × 1 SO4 SULFATE ION × 1 CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；281 K；well solution 2.3M ammonium sulphate, 100 mM citric acid pH 5.6 and 200 mM NaCl	Resolution 2.51 Å R-free 0.300
8AF3 Sterol carrier protein Artifical metalloenzyme incorporating Q111C mutation coupled to 2,2'-bipyridine Deposited 2022-07-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 618–736（119 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	TRT FRAGMENT OF TRITON X-100 × 1 SO4 SULFATE ION × 2 CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；278 K；well solution 2.3M ammonium sulphate, 100 mM citric acid pH 5.6 and 200 mM NaCl	Resolution 1.52 Å R-free 0.239

6 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DHB4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–120； UniProt 618–736

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	1ikt
Deposition date deposition_date	2001-05-07
Structure title title	LIGANDED STEROL CARRIER PROTEIN TYPE 2 (SCP-2) LIKE DOMAIN OF HUMAN MULTIFUNCTIONAL ENZYME TYPE 2 (MFE-2)
Keywords keywords	;alfa-beta fold, protein-Triton X-100 complex, hydrophobic tunnel, exposed peroxisomal targeting signal type 1 (PTS1), OXIDOREDUCTASE ;; OXIDOREDUCTASE
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	14.74 Å
Radius of gyration Rg (electron density) rg_electron	13.17 Å
Forward intensity I(0) i0	3290500.00
Molecular weight molecular_weight	13291.0 kDa
Excluded volume excluded_volume	16961 Å³
Envelope volume envelope_volume	18375 Å³
Hydration-shell volume shell_volume	11786 Å³
Envelope diameter envelope_diameter	44.1 Å
Shell Rg shell_rg	19.01 Å
Envelope Rg envelope_rg	13.38 Å
Shape Rg shape_rg	13.13 Å
Total Rg total_rg	14.63 Å
Total atoms total_atoms	933
Residues n_residues	115
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	45.0 Å
Rg (real space) rg_real	14.60 Å
Rg uncertainty (real space) rg_real_error	0.20 Å
I(0) (real space) i0_real	3.2910e+06
I(0) uncertainty (real space) i0_real_error	3.5610e+04
Rg (reciprocal space) rg_reciprocal	14.62 Å
I(0) (reciprocal space) i0_reciprocal	3291000.0000
Solution quality estimate total_estimate	0.8904
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	44.4 Å
Skewness Skewness skewness	-0.002
Kurtosis Kurtosis kurtosis	-0.381
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	644800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.979

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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	ESTRADIOL 17 BETA-DEHYDROGENASE 4
Molecular weight formula_weight	13264.5 kDa
EC 编号 ec_number	1.1.1.62
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	1059

MEGGKLQSTFVFEEIGRRLKDIGPEVVKKVNAVFEWHITKGGNIGAKWTIDLKSGSGKVYQGPAKGAADTTIILSDEDFMEVVLGKLDPQKAFFSGRLKARGNIMLSQKLQMILKDYAKL

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	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	OXTOXYNOL-10
Molecular weight formula_weight	646.8 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	126

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ikta_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.106 — SCP-like
Superfamily Superfamily superfamily	d.106.1 — SCP-like
Family Family family	d.106.1.1 — Sterol carrier protein, SCP

CATH v4.4 (1 domains)

Domain ID domain_id	1iktA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1050 — Nonspecific Lipid-transfer Protein; Chain A
Homologous superfamily homologous superfamily	10 — SCP2 sterol-binding domain

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8. Citations (1)

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Unit-cell length a length_a	35.474 Å
Unit-cell length b length_b	50.028 Å
Unit-cell length c length_c	62.725 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	1.750 Å
Low-resolution limit resolution_low	18.000 Å
R factor r_factor	—
R_work r_work	0.1920
R_free r_free	0.2140

fit	/app/data/saxs_computation/ik/1ikt/1ikt.fit
pddf	/app/data/pr_computation/ik/1ikt/1ikt.pr.out
profile	/app/data/saxs_computation/ik/1ikt/1ikt.dat

LIGANDED STEROL CARRIER PROTEIN TYPE 2 (SCP-2) LIKE DOMAIN OF HUMAN MULTIFUNCTIONAL ENZYME TYPE 2 (MFE-2)

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

ESTRADIOL 17 BETA-DEHYDROGENASE 4

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