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- PDB-3h6k: Crystal Structure of Human 11-beta-hydroxysteroid-dehydrogenase B... -

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Basic information

Entry
Database: PDB / ID: 3h6k
TitleCrystal Structure of Human 11-beta-hydroxysteroid-dehydrogenase Bound to an Ortho-chlro-sulfonyl-piperazine Inhibitor
ComponentsCorticosteroid 11-beta-dehydrogenase isozyme 1
KeywordsOXIDOREDUCTASE / HSD1 / NADP / inhibitor / Endoplasmic reticulum / Glycoprotein / Lipid metabolism / Membrane / Polymorphism / Signal-anchor / Steroid metabolism / Transmembrane
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-33T / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 11-beta-hydroxysteroid dehydrogenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.187 Å
AuthorsBard, J. / Svenson, K.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Efficacious 11beta-hydroxysteroid dehydrogenase type I inhibitors in the diet-induced obesity mouse model.
Authors: Wan, Z.K. / Chenail, E. / Xiang, J. / Li, H.Q. / Ipek, M. / Bard, J. / Svenson, K. / Mansour, T.S. / Xu, X. / Tian, X. / Suri, V. / Hahm, S. / Xing, Y. / Johnson, C.E. / Li, X. / Qadri, A. / ...Authors: Wan, Z.K. / Chenail, E. / Xiang, J. / Li, H.Q. / Ipek, M. / Bard, J. / Svenson, K. / Mansour, T.S. / Xu, X. / Tian, X. / Suri, V. / Hahm, S. / Xing, Y. / Johnson, C.E. / Li, X. / Qadri, A. / Panza, D. / Perreault, M. / Tobin, J.F. / Saiah, E.
History
DepositionApr 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 13, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)132,24112
Polymers127,3484
Non-polymers4,8938
Water2,684149
1
A: Corticosteroid 11-beta-dehydrogenase isozyme 1
B: Corticosteroid 11-beta-dehydrogenase isozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1206
Polymers63,6742
Non-polymers2,4474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-52 kcal/mol
Surface area19890 Å2
MethodPISA
2
C: Corticosteroid 11-beta-dehydrogenase isozyme 1
D: Corticosteroid 11-beta-dehydrogenase isozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1206
Polymers63,6742
Non-polymers2,4474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-52 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.198, 152.007, 74.543
Angle α, β, γ (deg.)90.000, 92.410, 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-beta-HSD1 / 11-DH


Mass: 31836.875 Da / Num. of mol.: 4 / Fragment: UNP residue 24-292, Lumenal / 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)
References: UniProt: P28845, 11beta-hydroxysteroid dehydrogenase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-33T / 3-chloro-4-({(2R)-4-[4-fluoro-2-(trifluoromethyl)phenyl]-2-methylpiperazin-1-yl}sulfonyl)benzamide


Mass: 479.876 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H18ClF4N3O3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 16.4 % PEG 3350, 100 mM MES, pH 7.1, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Mar 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.187→50 Å / Num. obs: 51709 / % possible obs: 80.9 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.065 / Χ2: 1.4 / Net I/σ(I): 15.173
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.187-2.282.20.37353771.6684.3
2.28-2.372.30.60753161.12183.8
2.37-2.482.30.41552031.10781.2
2.48-2.612.40.3149871.09478.4
2.61-2.772.40.24248121.27575.3
2.77-2.992.40.14747001.27973.5
2.99-3.292.40.09146351.36572.8
3.29-3.762.30.06249791.877.7
3.76-4.742.30.04255411.72686.5
4.74-502.60.03261591.5295.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
RefinementResolution: 2.187→31.471 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.41 / σ(F): 0.03 / Phase error: 34.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.275 2145 5.03 %
Rwork0.19 40479 -
obs0.194 42624 66.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.26 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso max: 177.56 Å2 / Biso mean: 49.628 Å2 / Biso min: 5.08 Å2
Baniso -1Baniso -2Baniso -3
1-6.081 Å2-0 Å2-2.932 Å2
2---2.984 Å2-0 Å2
3----3.097 Å2
Refinement stepCycle: LAST / Resolution: 2.187→31.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7841 0 316 149 8306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068307
X-RAY DIFFRACTIONf_angle_d1.08811283
X-RAY DIFFRACTIONf_chiral_restr0.0681318
X-RAY DIFFRACTIONf_plane_restr0.0041368
X-RAY DIFFRACTIONf_dihedral_angle_d20.4493006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.187-2.2380.4471240.3372528265262
2.238-2.2940.4161630.3132813297670
2.294-2.3560.421010.2832388248958
2.356-2.4250.371360.2552430256660
2.425-2.5030.3911160.2312348246458
2.503-2.5930.3531330.2232382251559
2.593-2.6960.3381360.2242269240556
2.696-2.8190.3161190.2282323244257
2.819-2.9670.3471230.2372351247458
2.967-3.1530.371400.2222372251259
3.153-3.3970.3321190.1942524264362
3.397-3.7380.2311620.1632975313773
3.738-4.2780.2251750.1423216339179
4.278-5.3850.2011980.1293740393891
5.385-31.4750.1942000.163820402092

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