5K6E | pdb_00005k6e

Crystal structure of Retinoic acid receptor-related orphan receptor (ROR) gamma ligand binding domain complex with SBI0654919

PDB DOI: https://doi.org/10.2210/pdb5K6E/pdb

Classification: transcription/transcription inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2016-05-24 Released: 2017-05-31
Deposition Author(s): Lu, J., Rastinejad, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.259 (Depositor), 0.261 (DCC)
R-Value Work:
0.209 (Depositor), 0.215 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of Retinoic acid receptor-related orphan receptor (ROR) gamma ligand binding domain complex with SBI0654919

Lu, J., Rastinejad, F.

To be published.

Macromolecule Content

Total Structure Weight: 58.43 kDa
Atom Count: 3,841
Modeled Residue Count: 460
Deposited Residue Count: 494
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor ROR-gamma	A, B	247	Homo sapiens	Mutation(s): 0 Gene Names: RORC, NR1F3, RORG, RZRG
UniProt & NIH Common Fund Data Resources
Find proteins for P51449 (Homo sapiens) Explore P51449 Go to UniProtKB: P51449
PHAROS: P51449 GTEx: ENSG00000143365
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P51449
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6QP Query on 6QP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	2-chloranyl-6-fluoranyl-~{N}-[(2~{R})-4-(4-fluorophenyl)sulfonyl-2-(hydroxymethyl)-2,3-dihydro-1,4-benzoxazin-6-yl]benzamide C₂₂ H₁₇ Cl F₂ N₂ O₅ S SLEGUDDXVCZXRA-OAHLLOKOSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.259 (Depositor), 0.261 (DCC)
R-Value Work: 0.209 (Depositor), 0.215 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.667	α = 90
b = 139.93	β = 90
c = 120.048	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-05-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-05-31
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.