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- PDB-3qqp: Crystal Structure of 11beta-Hydroxysteroid Dehydrogenase 1 (11b-H... -

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Basic information

Entry
Database: PDB / ID: 3qqp
TitleCrystal Structure of 11beta-Hydroxysteroid Dehydrogenase 1 (11b-HSD1) in Complex with Urea Inhibitor
ComponentsCorticosteroid 11-beta-dehydrogenase isozyme 1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / 11BETA / HYDROXYSTEROID / DEHYDROGENASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


11beta-hydroxysteroid dehydrogenase / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / cortisol dehydrogenase activity / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / Glucocorticoid biosynthesis / steroid catabolic process / Prednisone ADME / steroid binding / lung development ...11beta-hydroxysteroid dehydrogenase / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / cortisol dehydrogenase activity / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / Glucocorticoid biosynthesis / steroid catabolic process / Prednisone ADME / steroid binding / lung development / NADP binding / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / protein homodimerization activity / membrane
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Chem-S05 / 11-beta-hydroxysteroid dehydrogenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.72 Å
AuthorsLoenze, P. / Schimanski-Breves, S. / Engel, C.K.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Pyrrolidine-pyrazole ureas as potent and selective inhibitors of 11beta-hydroxysteroid-dehydrogenase type 1.
Authors: Venier, O. / Pascal, C. / Braun, A. / Namane, C. / Mougenot, P. / Crespin, O. / Pacquet, F. / Mougenot, C. / Monseau, C. / Onofri, B. / Dadji-Faihun, R. / Leger, C. / Ben-Hassine, M. / Van- ...Authors: Venier, O. / Pascal, C. / Braun, A. / Namane, C. / Mougenot, P. / Crespin, O. / Pacquet, F. / Mougenot, C. / Monseau, C. / Onofri, B. / Dadji-Faihun, R. / Leger, C. / Ben-Hassine, M. / Van-Pham, T. / Ragot, J.L. / Philippo, C. / Gussregen, S. / Engel, C. / Farjot, G. / Noah, L. / Maniani, K. / Nicolai, E.
History
DepositionFeb 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Corticosteroid 11-beta-dehydrogenase isozyme 1
B: Corticosteroid 11-beta-dehydrogenase isozyme 1
C: Corticosteroid 11-beta-dehydrogenase isozyme 1
D: Corticosteroid 11-beta-dehydrogenase isozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,57112
Polymers127,3484
Non-polymers4,2238
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16780 Å2
ΔGint-131 kcal/mol
Surface area39470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.927, 153.385, 74.179
Angle α, β, γ (deg.)90.000, 93.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Corticosteroid 11-beta-dehydrogenase isozyme 1 / 11-beta-hydroxysteroid dehydrogenase 1 / 11-DH / 11-beta-HSD1


Mass: 31836.875 Da / Num. of mol.: 4 / Mutation: C272S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD11, HSD11B1, HSD11L / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10
References: UniProt: P28845, 11beta-hydroxysteroid dehydrogenase
#2: Chemical
ChemComp-S05 / 3,4-dihydroquinolin-1(2H)-yl[4-(1H-imidazol-5-yl)piperidin-1-yl]methanone


Mass: 310.393 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H22N4O
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: 40% PEG300, 0.1M MES, pH 6.5, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.95373 Å
DetectorDate: Aug 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.72→74.12 Å / Num. obs: 34037 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Biso Wilson estimate: 28.411 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 11.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.72-2.820.3454.213438347299.6
2.82-2.940.3134.6413929359699.7
2.94-3.080.2555.5813404346399.7
3.08-3.240.2076.8812852332299.7
3.24-3.420.1578.8611582299199.8
3.42-3.640.13110.211277291599.8
3.64-3.910.10612.2810570274499.9
3.91-4.250.08414.296512527100
4.25-4.690.0716.548747230099.8
4.69-5.320.06617.5281542112100
5.32-6.280.07416.9969141793100
6.28-8.030.0522.955911454100
8.03-12.750.02932.883838100499.9
12.750.02934.96124534498.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
BUSTER-TNTBUSTER 2.9.7refinement
PDB_EXTRACT3.1data extraction
REFMACphasing
BUSTER2.9.7refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.72→36.71 Å / Cor.coef. Fo:Fc: 0.9345 / Cor.coef. Fo:Fc free: 0.88 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): -3
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 1683 4.95 %RANDOM
Rwork0.1644 ---
obs0.1678 34021 99.8 %-
all-34033 --
Displacement parametersBiso max: 144.9 Å2 / Biso mean: 29.5253 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-0.7124 Å20 Å2-0.4748 Å2
2---0.4555 Å20 Å2
3----0.2569 Å2
Refine analyzeLuzzati coordinate error obs: 0.272 Å
Refinement stepCycle: LAST / Resolution: 2.72→36.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8107 0 284 195 8586
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d30592
X-RAY DIFFRACTIONt_trig_c_planes1992
X-RAY DIFFRACTIONt_gen_planes12705
X-RAY DIFFRACTIONt_it864320
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion11185
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact105774
X-RAY DIFFRACTIONt_bond_d864320.01
X-RAY DIFFRACTIONt_angle_deg1172421.23
X-RAY DIFFRACTIONt_omega_torsion2.9
X-RAY DIFFRACTIONt_other_torsion19.42
LS refinement shellResolution: 2.72→2.8 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2819 167 5.69 %
Rwork0.1876 2769 -
all0.1932 2936 -
obs--99.8 %

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