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- PDB-5za1: Ligand complex of RORgt LBD -

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Basic information

Entry
Database: PDB / ID: 5za1
TitleLigand complex of RORgt LBD
ComponentsNuclear receptor ROR-gamma
KeywordsTRANSCRIPTION / RORgt LIGAND / RORgt inhibitor / STRUCTURE-BASED DESIGN
Function / homology
Function and homology information


ligand-activated transcription factor activity / cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / Peyer's patch development / positive regulation of circadian rhythm / oxysterol binding / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process ...ligand-activated transcription factor activity / cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / Peyer's patch development / positive regulation of circadian rhythm / oxysterol binding / T-helper cell differentiation / 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-9A0 / DIMETHYLFORMAMIDE / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsYamamoto, S. / Yamaguchi, H.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2018
Title: Discovery of a potent orally bioavailable retinoic acid receptor-related orphan receptor-gamma-t (ROR gamma t) inhibitor, S18-000003.
Authors: Sasaki, Y. / Odan, M. / Yamamoto, S. / Kida, S. / Ueyama, A. / Shimizu, M. / Haruna, T. / Watanabe, A. / Okuno, T.
History
DepositionFeb 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,05515
Polymers54,4212
Non-polymers1,63413
Water1,78399
1
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0588
Polymers27,2101
Non-polymers8487
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9967
Polymers27,2101
Non-polymers7866
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.501, 97.501, 128.114
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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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: 27210.471 Da / Num. of mol.: 2 / Fragment: UNP residues 265-494
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) / References: UniProt: P51449
#2: Chemical ChemComp-9A0 / 2-[4-({[4-(ethylsulfonyl)phenyl]acetyl}amino)phenyl]-2-methyl-N-phenylpropanamide


Mass: 464.577 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H28N2O4S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 3.32 Å3/Da / Density % sol: 62.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M BisTris propane pH6.5, 0.9M Ammonium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.52→50 Å / Num. obs: 23398 / % possible obs: 99.2 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 31.4
Reflection shellResolution: 2.52→2.61 Å / Rmerge(I) obs: 0.487 / Num. unique obs: 4441

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B0W

3b0w


Resolution: 2.52→48.75 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.904 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.367 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2558 1192 5.1 %RANDOM
Rwork0.1863 ---
obs0.1897 21988 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.56 Å2 / Biso mean: 46.412 Å2 / Biso min: 25.61 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.52→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3633 0 112 99 3844
Biso mean--45.56 42.76 -
Num. residues----454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193825
X-RAY DIFFRACTIONr_bond_other_d00.023552
X-RAY DIFFRACTIONr_angle_refined_deg2.091.9725142
X-RAY DIFFRACTIONr_angle_other_deg3.74138191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0685456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92723.446177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.14715679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3881526
X-RAY DIFFRACTIONr_chiral_restr0.2560.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024200
X-RAY DIFFRACTIONr_gen_planes_other0.0230.02826
X-RAY DIFFRACTIONr_mcbond_it3.4124.5641822
X-RAY DIFFRACTIONr_mcbond_other3.374.561819
X-RAY DIFFRACTIONr_mcangle_it5.0436.8282272
LS refinement shellResolution: 2.52→2.585 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 89 -
Rwork0.236 1609 -
all-1698 -
obs--98.15 %

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