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- PDB-5apk: Ligand complex of RORg LBD -

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Basic information

Entry
Database: PDB / ID: 5apk
TitleLigand complex of RORg LBD
Components(NUCLEAR RECEPTOR ROR-GAMMA) x 2
KeywordsTRANSCRIPTION / RORG LIGAND / RORG AGONIST / STRUCTURE-BASED DESIGN
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 / T-helper cell differentiation / positive regulation of circadian rhythm / oxysterol binding / 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 / T-helper cell differentiation / positive regulation of circadian rhythm / oxysterol binding / 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-76E / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsXue, Y. / Aagaard, A. / Narjes, F.
CitationJournal: ChemMedChem / Year: 2016
Title: Benzoxazepines Achieve Potent Suppression of IL-17 Release in Human T-Helper 17 (TH 17) Cells through an Induced-Fit Binding Mode to the Nuclear Receptor ROR gamma.
Authors: Olsson, R.I. / Xue, Y. / von Berg, S. / Aagaard, A. / McPheat, J. / Hansson, E.L. / Bernstrom, J. / Hansson, P. / Jirholt, J. / Grindebacke, H. / Leffler, A. / Chen, R. / Xiong, Y. / Ge, H. ...Authors: Olsson, R.I. / Xue, Y. / von Berg, S. / Aagaard, A. / McPheat, J. / Hansson, E.L. / Bernstrom, J. / Hansson, P. / Jirholt, J. / Grindebacke, H. / Leffler, A. / Chen, R. / Xiong, Y. / Ge, H. / Hansson, T.G. / Narjes, F.
History
DepositionSep 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: NUCLEAR RECEPTOR ROR-GAMMA
B: NUCLEAR RECEPTOR ROR-GAMMA
D: NUCLEAR RECEPTOR ROR-GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5285
Polymers63,4703
Non-polymers1,0582
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-19.6 kcal/mol
Surface area22690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.750, 99.750, 129.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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 / RORG


Mass: 30918.490 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, UNP RESIDUES 265-507
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P51449
#2: Protein/peptide 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 / RORG


Mass: 1632.925 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 480-492
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P51449
#3: Chemical ChemComp-76E / 2-CHLORO-6-FLUORO-N-[4-[3-(TRIFLUOROMETHYL)PHENYL]SULFONYL-3,5-DIHYDRO-2H-1,4-BENZOXAZEPIN-7-YL]BENZAMIDE


Mass: 528.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H17ClF4N2O4S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details2-CHLORO-6-FLUORO-N-[4-[3-(TRIFLUOROMETHYL)PHENYL]SULFONYL-3,5-DIHYD

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.03 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.1→46.54 Å / Num. obs: 42558 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Biso Wilson estimate: 43.49 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 10
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 0.9 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L0L
Resolution: 2.1→46.54 Å / Cor.coef. Fo:Fc: 0.9384 / Cor.coef. Fo:Fc free: 0.9352 / SU R Cruickshank DPI: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.169 / SU Rfree Blow DPI: 0.148 / SU Rfree Cruickshank DPI: 0.149
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 2227 5.24 %RANDOM
Rwork0.1962 ---
obs0.1977 42530 99.93 %-
Displacement parametersBiso mean: 50.39 Å2
Baniso -1Baniso -2Baniso -3
1--3.2549 Å20 Å20 Å2
2---3.2549 Å20 Å2
3---6.5099 Å2
Refine analyzeLuzzati coordinate error obs: 0.245 Å
Refinement stepCycle: LAST / Resolution: 2.1→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3912 0 70 303 4285
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014069HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.085488HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1464SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes98HARMONIC2
X-RAY DIFFRACTIONt_gen_planes606HARMONIC5
X-RAY DIFFRACTIONt_it4069HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion19.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion498SEMIHARMONIC5
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_contact4796SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 187 6.07 %
Rwork0.2386 2892 -
all0.2405 3079 -
obs--99.93 %

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