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- PDB-4zom: RORgamma in complex with inverse agonist 4j. -

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Basic information

Entry
Database: PDB / ID: 4zom
TitleRORgamma in complex with inverse agonist 4j.
ComponentsNuclear receptor ROR-gamma
KeywordsTRANSCRIPTION / RORgamma Inverse Agonist
Function / homology
Function and homology information


T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / Peyer's patch development / oxysterol binding / T-helper cell differentiation / positive regulation of circadian rhythm / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process ...T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / Peyer's patch development / oxysterol binding / T-helper cell differentiation / positive regulation of circadian rhythm / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process / regulation of fat cell differentiation / regulation of glucose metabolic process / lymph node development / adipose tissue development / xenobiotic metabolic process / circadian regulation of gene expression / DNA-binding transcription repressor activity, RNA polymerase II-specific / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / Interleukin-4 and Interleukin-13 signaling / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors ...Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-4Q3 / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsMarcotte, D.J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: Discovery of novel pyrazole-containing benzamides as potent ROR gamma inverse agonists.
Authors: Wang, T. / Banerjee, D. / Bohnert, T. / Chao, J. / Enyedy, I. / Fontenot, J. / Guertin, K. / Jones, H. / Lin, E.Y. / Marcotte, D. / Talreja, T. / Van Vloten, K.
History
DepositionMay 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Data collection
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear receptor ROR-gamma
B: Nuclear receptor ROR-gamma
C: Nuclear receptor ROR-gamma
D: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,6818
Polymers104,6414
Non-polymers2,0404
Water86548
1
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6702
Polymers26,1601
Non-polymers5101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6702
Polymers26,1601
Non-polymers5101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6702
Polymers26,1601
Non-polymers5101
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6702
Polymers26,1601
Non-polymers5101
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.422, 99.422, 129.439
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
DetailsMonomer confirmed by SEC

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Components

#1: Protein
Nuclear receptor ROR-gamma / Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / RAR-related orphan ...Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / RAR-related orphan receptor C / Retinoid-related orphan receptor-gamma


Mass: 26160.232 Da / Num. of mol.: 4 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RORC, NR1F3, RORG, RZRG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P51449
#2: Chemical
ChemComp-4Q3 / N-{4-[3-(acetylamino)-1-(propan-2-yl)-1H-pyrazol-5-yl]-2-[(1R,5S)-3-azabicyclo[3.1.0]hex-3-yl]phenyl}-2-chloro-6-fluoro-N-methylbenzamide


Mass: 510.003 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H29ClFN5O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 3.53 Å3/Da / Density % sol: 65.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M TRIS pH 8.0, 1.8M Na formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.536
11-h,-k,l20.464
ReflectionResolution: 2.27→19.791 Å / Num. obs: 65964 / % possible obs: 99.7 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.146 / Rsym value: 0.146 / Net I/av σ(I): 3.861 / Net I/σ(I): 7.4 / Num. measured all: 386328
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym valueNet I/σ(I) obs% possible all
2.27-2.395.80.8550.85619496940.8552.4100
2.39-2.545.80.5811.25301091020.5813.4100
2.54-2.715.80.4081.75017185850.4084.6100
2.71-2.935.90.2532.74710980270.2536.2100
2.93-3.215.90.1614.64334873620.1618.2100
3.21-3.595.90.1055.93910966250.10510.3100
3.59-4.145.90.1025.63475358740.10212.1100
4.14-5.085.90.115.52929749420.1113.1100
5.08-7.185.90.0886.92284038450.08813.2100
7.18-19.7915.50.04713.51049719080.04713.891.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
SCALAdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BOW

3bow


Resolution: 2.27→19.79 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / SU B: 9.526 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 3396 5.2 %RANDOM
Rwork0.2003 ---
obs0.2023 62513 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.65 Å2 / Biso mean: 41.14 Å2 / Biso min: 16.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2--0.5 Å20 Å2
3----1 Å2
Refinement stepCycle: final / Resolution: 2.27→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7053 0 144 48 7245
Biso mean--39.78 40.73 -
Num. residues----879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.0197367
X-RAY DIFFRACTIONr_bond_other_d0.0070.027007
X-RAY DIFFRACTIONr_angle_refined_deg2.5051.9729951
X-RAY DIFFRACTIONr_angle_other_deg1.528316021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8115877
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24523.2350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.465151306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6921557
X-RAY DIFFRACTIONr_chiral_restr0.1860.21091
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.028317
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021834
X-RAY DIFFRACTIONr_mcbond_it4.0393.7693525
X-RAY DIFFRACTIONr_mcbond_other4.0333.7693516
X-RAY DIFFRACTIONr_mcangle_it5.5495.634395
LS refinement shellResolution: 2.27→2.328 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 247 -
Rwork0.313 4561 -
all-4808 -
obs--99.59 %
Refinement TLS params.Method: refined / Origin x: 23.4386 Å / Origin y: 182.8109 Å / Origin z: 3.3418 Å
111213212223313233
T0.0042 Å2-0.0013 Å2-0.0031 Å2-0.0045 Å20.0042 Å2--0.006 Å2
L0.0116 °2-0.0127 °20.0025 °2-0.0222 °2-0.0151 °2--0.0249 °2
S0.0003 Å °0.0001 Å °-0.0015 Å °0.0017 Å °0.0014 Å °0.0045 Å °-0.0023 Å °0.0028 Å °-0.0017 Å °

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