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3hb5

Binary and ternary crystal structures of a novel inhibitor of 17 beta-HSD type 1: a lead compound for breast cancer therapy

Method: X-RAY DIFFRACTION Dmax: 65.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Estradiol 17-beta-dehydrogenase 1

OrganismNot specified

UniProt P14061

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 X； UniProt 2–328 Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 E2B 3-{[(9beta,14beta,16alpha,17alpha)-3,17-dihydroxyestra-1,3,5(10)-trien-16-yl]methyl}benzamide × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；300 K；pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K Resolution 2.00 Å R-free 0.248

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 3HB5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A27 HUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 C-TERMINAL DELETION MUTANT COMPLEXED WITH ESTRADIOL AND NADP+ Deposited 1998-01-16 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 1–289（289 aa）
Mutation：C-TERMINAL DELETION (290 - 327) EST ESTRADIOL × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.1；PROTEIN WAS CRYSTALLIZED FROM 12-16 % PEG4000, 100 MM HEPES PH 7.1, 0.5 MM ESTRADIOL, 200 MM NACL, 100MM MGCL2, 2.2 MM DECYL-BETA-D-MALTOSIDE; THEN SOAKED IN 30 % PEG 4000, 100 MM HEPES PH 7.1, 100 MM MGCL2, 0.5 MM ESTRADIOL, 1 MM NADP+
Resolution 1.90 Å R-free 0.261
1BHS HUMAN ESTROGENIC 17BETA-HYDROXYSTEROID DEHYDROGENASE Deposited 1995-04-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–327（327 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å R-free 0.229
1DHT ESTROGENIC 17-BETA HYDROXYSTEROID DEHYDROGENASE COMPLEXED DIHYDROTESTOSTERONE Deposited 1998-03-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–327（327 aa）
Not recorded DHT 5-ALPHA-DIHYDROTESTOSTERONE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；pH 7.20
Resolution 2.24 Å R-free 0.279
1EQU TYPE 1 17-BETA HYDROXYSTEROID DEHYDROGENASE EQUILIN COMPLEXED WITH NADP+ Deposited 1998-12-02 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 1–327（327 aa）
Chain B 1–327（327 aa）
Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 EQI EQUILIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；VAP. DIFF. FROM 28% PEG 4000 IN HEPES BUFFER, PH 7.5, CONTAINING 1 MM EQUILIN, pH 7.50
Resolution 3.00 Å R-free 0.315
1FDS HUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 COMPLEXED WITH 17-BETA-ESTRADIOL Deposited 1996-06-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–327（327 aa）
Not recorded EST ESTRADIOL × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.70 Å R-free 0.203
1FDT HUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 COMPLEXED WITH ESTRADIOL AND NADP+ Deposited 1996-06-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–327（327 aa）
Not recorded SO4 SULFATE ION × 2 EST ESTRADIOL × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å R-free 0.243
1FDU HUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 MUTANT H221L COMPLEXED WITH ESTRADIOL AND NADP+ Deposited 1998-01-14 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 1–327（327 aa）
Chain B 1–327（327 aa）
Mutation：H221L Mutation：H221L SO4 SULFATE ION × 2 EST ESTRADIOL × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.3；PROTEIN WAS CRYSTALLIZED FROM 2 M AMMONIUM SULFATE, 100 MM SODIUM PHOSPHATE BUFFER PH 6.3, 1 MM NADP+, 100 MM NACL; THEN SOAKED IN 30 % PEG 4000, 100 MM HEPES PH 6.5, 100 MM NACL, 0.5 MM ESTRADIOL, 1 MM NADP+
Resolution 2.70 Å R-free 0.295
1FDU HUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 MUTANT H221L COMPLEXED WITH ESTRADIOL AND NADP+ Deposited 1998-01-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–327（327 aa）
Chain D 1–327（327 aa）
Mutation：H221L Mutation：H221L SO4 SULFATE ION × 2 EST ESTRADIOL × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.3；PROTEIN WAS CRYSTALLIZED FROM 2 M AMMONIUM SULFATE, 100 MM SODIUM PHOSPHATE BUFFER PH 6.3, 1 MM NADP+, 100 MM NACL; THEN SOAKED IN 30 % PEG 4000, 100 MM HEPES PH 6.5, 100 MM NACL, 0.5 MM ESTRADIOL, 1 MM NADP+
Resolution 2.70 Å R-free 0.295
1FDV HUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 MUTANT H221L COMPLEXED WITH NAD+ Deposited 1998-01-15 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 1–327（327 aa）
Chain B 1–327（327 aa）
Mutation：H221L Mutation：H221L SO4 SULFATE ION × 2 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.3；PROTEIN WAS CRYSTALLIZED FROM 2 M AMMONIUM SULFATE, 100 MM SODIUM PHOSPHATE BUFFER PH 6.3, 1 MM NAD+, 100 MM NACL; THEN SOAKED IN 27 % GLYCEROL, 2.3 M AMMONIUM SULFATE, 100 MM SODIUM PHOSPHATE BUFFER PH 6.1, 80 MM NACL, 1 MM NAD+
Resolution 3.10 Å R-free 0.295
1FDV HUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 MUTANT H221L COMPLEXED WITH NAD+ Deposited 1998-01-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–327（327 aa）
Chain D 1–327（327 aa）
Mutation：H221L Mutation：H221L SO4 SULFATE ION × 2 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.3；PROTEIN WAS CRYSTALLIZED FROM 2 M AMMONIUM SULFATE, 100 MM SODIUM PHOSPHATE BUFFER PH 6.3, 1 MM NAD+, 100 MM NACL; THEN SOAKED IN 27 % GLYCEROL, 2.3 M AMMONIUM SULFATE, 100 MM SODIUM PHOSPHATE BUFFER PH 6.1, 80 MM NACL, 1 MM NAD+
Resolution 3.10 Å R-free 0.295
1FDW HUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 MUTANT H221Q COMPLEXED WITH ESTRADIOL Deposited 1998-01-16 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 1–327（327 aa）
Mutation：H221Q EST ESTRADIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PROTEIN WAS CRYSTALLIZED FROM PEG 4000 30%, 100 MM HEPES BUFFER PH 7.0, 100 MM MGCL2, 0.5 MM ESTRADIOL, PROPANE DIOL 2-4%
Resolution 2.70 Å R-free 0.263
1I5R TYPE 1 17-BETA HYDROXYSTEROID DEHYDROGENASE EM1745 COMPLEX Deposited 2001-02-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–327（327 aa）
Not recorded HYC O5'-[9-(3,17B-DIHYDROXY-1,3,5(10)-ESTRATRIEN-16B-YL)-NONANOYL]ADENOSINE × 2 GOL GLYCEROL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；PEG3500, GLYCEROL, SODIUM CHLORIDE, BETA-OCTYL GLUCOSIDE, DITHIOTHREITOL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 1.60 Å R-free 0.205
1I5R TYPE 1 17-BETA HYDROXYSTEROID DEHYDROGENASE EM1745 COMPLEX Deposited 2001-02-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–327（327 aa）
Not recorded HYC O5'-[9-(3,17B-DIHYDROXY-1,3,5(10)-ESTRATRIEN-16B-YL)-NONANOYL]ADENOSINE × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；PEG3500, GLYCEROL, SODIUM CHLORIDE, BETA-OCTYL GLUCOSIDE, DITHIOTHREITOL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 1.60 Å R-free 0.205
1IOL ESTROGENIC 17-BETA HYDROXYSTEROID DEHYDROGENASE COMPLEXED 17-BETA-ESTRADIOL Deposited 1996-06-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–327（327 aa）
Not recorded EST ESTRADIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 2.30 Å R-free 0.257
1JTV Crystal structure of 17beta-Hydroxysteroid Dehydrogenase Type 1 complexed with Testosterone Deposited 2001-08-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–327（327 aa）
Not recorded TES TESTOSTERONE × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；300 K；PEG 4000,magnesium chloride,beta-octylglucoside,glycerol,Hepes,soaking with testosterone, pH 7.5, temperature 300K
Resolution 1.54 Å R-free 0.208
1QYV Crystal structure of human estrogenic 17beta-hydroxysteroid dehydrogenase complex with NADP Deposited 2003-09-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–327（327 aa）
Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；300 K；PEG4000, magnisum chloride, beta-octylglucoside, HEPES, glycerol, soaking with NADP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 1.81 Å R-free 0.235
1QYW Crystal structure of human estrogenic 17beta-hydroxysteroid dehydrogenase complex with androstanedione and NADP Deposited 2003-09-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–327（327 aa）
Not recorded 5SD 5ALPHA-ANDROSTAN-3,17-DIONE × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；300 K；PEG 4000, magnisum chloride, beta-octylglucoside, HEPES, glycerol, soaking with dihydrotestosterone and NADP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 1.63 Å R-free 0.249
1QYX Crystal structure of human estrogenic 17beta-hydroxysteroid dehydrogenase complex with androstenedione and NADP Deposited 2003-09-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–327（327 aa）
Not recorded ASD 4-ANDROSTENE-3-17-DIONE × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；300 K；PEG 4000, magnisum chloride, beta-octylglucoside, HEPES, glycerol, soaking with testosterone and NADP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 1.89 Å R-free 0.227
3DEY Crystal structure of 17beta-HSD1 with DHT in normal and reverse orientation. Deposited 2008-06-10 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain X 2–328（327 aa）
Not recorded DHT 5-ALPHA-DIHYDROTESTOSTERONE × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 1.70 Å R-free 0.257
3DHE ESTROGENIC 17-BETA HYDROXYSTEROID DEHYDROGENASE COMPLEXED DEHYDROEPIANDROSTERONE Deposited 1998-03-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–327（327 aa）
Not recorded AND 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；pH 7.20
Resolution 2.30 Å R-free 0.249
3HB4 17beta-hydroxysteroid dehydrogenase type1 complexed with E2B Deposited 2009-05-04 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain X 2–328（327 aa）
Not recorded E2B 3-{[(9beta,14beta,16alpha,17alpha)-3,17-dihydroxyestra-1,3,5(10)-trien-16-yl]methyl}benzamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；300 K；pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 2.21 Å R-free 0.257
3KLM 17beta-HSD1 in complex with DHT Deposited 2009-11-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain X 2–328（327 aa）
Not recorded DHT 5-ALPHA-DIHYDROTESTOSTERONE × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 1.70 Å R-free 0.257
3KLP 17beta-HSD1 in complex with A-diol Deposited 2009-11-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain X 2–328（327 aa）
Not recorded B81 (3alpha,8alpha,17beta)-androst-5-ene-3,17-diol × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.254
3KM0 17betaHSD1 in complex with 3beta-diol Deposited 2009-11-09 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 2–328（327 aa）
Chain B 2–328（327 aa）
Not recorded AOM 5-ALPHA-ANDROSTANE-3-BETA,17BETA-DIOL × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.30 Å R-free 0.312
6CGC Crystal structure of human 17beta-HSD type 1 in ternary complex with 2-MeO-CC-156 and NADP+ Deposited 2018-02-19 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 1–328（328 aa）
Chain B 1–328（328 aa）
Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 F0A 3-{[(9beta,14beta,16alpha,17alpha)-3,17-dihydroxy-2-methoxyestra-1,3,5(10)-trien-16-yl]methyl}benzamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；300 K；PEG 8000, potassium phosphate monobasic
Resolution 2.10 Å R-free 0.260
6CGE Crystal structure of human 17beta-HSD type 1 in ternary complex with PBRM and NADP+ Deposited 2018-02-20 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 1–328（328 aa）
Chain B 1–328（328 aa）
Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 F0D 3-{[(14beta,16alpha,17alpha)-3-(2-bromoethyl)-17-hydroxyestra-1,3,5(10)-trien-16-yl]methyl}benzamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；300 K；PEG 8000, potassium phosphate monobasic
Resolution 2.20 Å R-free 0.303
6DTP CRYSTAL STRUCTURE OF HUMAN 17BETA-HYDROXYSTEROID DEHYDROGENASE TYPE 1 COMPLEXED WITH EM139 Deposited 2018-06-18 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 1–328（328 aa）
Chain B 1–328（328 aa）
Not recorded GOL GLYCEROL × 7 EDO 1,2-ETHANEDIOL × 4 EM9 N-butyl-11-[(7alpha,9beta,13alpha,14beta,16alpha,17alpha)-16-chloro-3,17-dihydroxyestra-1,3,5(10)-trien-7-yl]-N-methylundecanamide × 1 PGE TRIETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；MgCl2, PEG4000
Resolution 2.00 Å R-free 0.234
6MNC CRYSTAL STRUCTURE OF HUMAN 17BETA-HYDROXYSTEROID DEHYDROGENASE TYPE 1 COMPLEXED WITH ESTRONE Deposited 2018-10-01 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 1–328（328 aa）
Chain B 1–328（328 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 J3Z (9beta,13alpha)-3-hydroxyestra-1,3,5(10)-trien-17-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；MgCl2, PEG3350, Glycerol
Resolution 2.40 Å R-free 0.287
6MNE CRYSTAL STRUCTURE OF HUMAN 17BETA-HYDROXYSTEROID DEHYDROGENASE TYPE 1 COMPLEXED WITH ESTRONE AND NADP+ Deposited 2018-10-01 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 1–328（328 aa）
Chain B 1–328（328 aa）
Not recorded NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 J3Z (9beta,13alpha)-3-hydroxyestra-1,3,5(10)-trien-17-one × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；300 K；KH2PO4, PEG8000
Resolution 1.86 Å R-free 0.223
7X3Z Crystal structure of human 17beta-hydroxysteroid dehydrogenase type 1 complexed with estrone and NAD Deposited 2022-03-01 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 1–328（328 aa）
Chain B 1–328（328 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 J3Z (9beta,13alpha)-3-hydroxyestra-1,3,5(10)-trien-17-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；KH2PO4, PEG 8000
Resolution 2.25 Å R-free 0.255

27 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DHB1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain X； PDBConstruct 1–327； UniProt 2–328

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

SAXS profile for 3hb5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3hb5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3hb5
Deposition date deposition_date2009-05-04
Structure title titleBinary and ternary crystal structures of a novel inhibitor of 17 beta-HSD type 1: a lead compound for breast cancer therapy
Keywords keywords17beta-HSD1, Cytoplasm, Lipid synthesis, NADP, Oxidoreductase, Polymorphism, Steroid biosynthesis; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.47 Å
Radius of gyration Rg (electron density) rg_electron19.41 Å
Forward intensity I(0) i017918400.00
Molecular weight molecular_weight32128.0 kDa
Excluded volume excluded_volume40303 ų
Envelope volume envelope_volume46882 ų
Hydration-shell volume shell_volume20256 ų
Envelope diameter envelope_diameter67.6 Å
Shell Rg shell_rg25.70 Å
Envelope Rg envelope_rg19.73 Å
Shape Rg shape_rg19.45 Å
Total Rg total_rg20.16 Å
Total atoms total_atoms2255
Residues n_residues284
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax65.4 Å
Rg (real space) rg_real20.42 Å
Rg uncertainty (real space) rg_real_error0.47 Å
I(0) (real space) i0_real1.7920e+07
I(0) uncertainty (real space) i0_real_error2.2220e+05
Rg (reciprocal space) rg_reciprocal20.43 Å
I(0) (reciprocal space) i0_reciprocal17920000.0000
Solution quality estimate total_estimate0.8134
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.2 Å
Skewness Skewness skewness0.305
Kurtosis Kurtosis kurtosis-0.321
Angular range angular_range— – 0.3900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3329000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.857; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3hb5x_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.2 — Tyrosine-dependent oxidoreductases

CATH v4.4 (1 domains)

Domain ID domain_id3hb5X00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
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8. Citations (1)

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9. Files and Curves (10)