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

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Basic information

Entry
Database: PDB / ID: 3fco
TitleCrystal Structure of 11beta-Hydroxysteroid Dehydrogenase 1 (11b-HSD1) in Complex with Benzamide Inhibitor
ComponentsCorticosteroid 11-beta-dehydrogenase isozyme 1
KeywordsOXIDOREDUCTASE / Endoplasmic reticulum / Glycoprotein / Lipid metabolism / Membrane / NADP / 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-IIG / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 11-beta-hydroxysteroid dehydrogenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsWang, Z. / Sudom, A. / Walker, N.P.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Optimization of novel di-substituted cyclohexylbenzamide derivatives as potent 11 beta-HSD1 inhibitors.
Authors: McMinn, D.L. / Rew, Y. / Sudom, A. / Caille, S. / Degraffenreid, M. / He, X. / Hungate, R. / Jiang, B. / Jaen, J. / Julian, L.D. / Kaizerman, J. / Novak, P. / Sun, D. / Tu, H. / Ursu, S. / ...Authors: McMinn, D.L. / Rew, Y. / Sudom, A. / Caille, S. / Degraffenreid, M. / He, X. / Hungate, R. / Jiang, B. / Jaen, J. / Julian, L.D. / Kaizerman, J. / Novak, P. / Sun, D. / Tu, H. / Ursu, S. / Walker, N.P. / Yan, X. / Ye, Q. / Wang, Z. / Powers, J.P.
History
DepositionNov 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.3Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,9836
Polymers63,6742
Non-polymers2,3104
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7770 Å2
ΔGint-58 kcal/mol
Surface area21770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.185, 109.185, 135.869
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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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.: 2 / Mutation: C272S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD11B1, HSD11, HSD11L / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): DH10a
References: UniProt: P28845, 11beta-hydroxysteroid dehydrogenase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-IIG / N-cyclopropyl-N-(cis-4-cyclopropyl-4-hydroxycyclohexyl)-4-[(1S)-2,2,2-trifluoro-1-hydroxy-1-methylethyl]benzamide


Mass: 411.458 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H28F3NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 3.95 Å3/Da / Density % sol: 68.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5
Details: 36% P400, 0.1 M Tris 8.5, vapor diffusion, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2005 / Details: 3X3 CCD ARRAY
RadiationMonochromator: DOUBLE-CRYSTAL, SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→94.557 Å / Num. obs: 27575 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 78.93 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 7.187
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.65-2.797.10.36122860640100.361100
2.79-2.967.10.233.12679537800.23100
2.96-3.177.10.1494.62509535580.149100
3.17-3.4270.0996.62326933220.099100
3.42-3.756.90.0777.72122030640.07799.9
3.75-4.196.90.0668.31907127820.06699.9
4.19-4.846.60.0589.51645424930.058100
4.84-5.935.80.0510.31225120950.0599.6
5.93-8.387.10.04711.51173716640.04799.6
8.38-94.4960.03119.248568070.03183.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å40.76 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
BOSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→94.49 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.266 / WRfactor Rwork: 0.239 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.797 / SU B: 9.768 / SU ML: 0.206 / SU R Cruickshank DPI: 0.423 / SU Rfree: 0.281 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.423 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1378 5 %RANDOM
Rwork0.222 ---
obs0.224 27430 98.88 %-
all-27778 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 136.04 Å2 / Biso mean: 65.341 Å2 / Biso min: 33.79 Å2
Baniso -1Baniso -2Baniso -3
1-2.47 Å21.24 Å20 Å2
2--2.47 Å20 Å2
3----3.71 Å2
Refinement stepCycle: LAST / Resolution: 2.65→94.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4123 0 154 51 4328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224365
X-RAY DIFFRACTIONr_angle_refined_deg2.0352.0065930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6225537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07323.939165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.85115762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3981520
X-RAY DIFFRACTIONr_chiral_restr0.1680.2691
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213120
X-RAY DIFFRACTIONr_mcbond_it0.8431.52651
X-RAY DIFFRACTIONr_mcangle_it1.58824262
X-RAY DIFFRACTIONr_scbond_it2.1331714
X-RAY DIFFRACTIONr_scangle_it3.5424.51652
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 89 -
Rwork0.327 1931 -
all-2020 -
obs-28606 99.56 %

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