5K3M | pdb_00005k3m

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

PDB DOI: https://doi.org/10.2210/pdb5K3M/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-05-19 Released: 2017-05-31
Deposition Author(s): Huang, P., Rastinejad, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free:
0.295 (Depositor), 0.315 (DCC)
R-Value Work:
0.265 (Depositor), 0.280 (DCC)
R-Value Observed:
0.268 (Depositor)

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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 UUA

Lu, J., Rastinejad, F.

To be published.

Macromolecule Content

Total Structure Weight: 58.36 kDa
Atom Count: 3,692
Modeled Residue Count: 444
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
6Q5 Query on 6Q5 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]	Ursolic acid C₃₀ H₄₈ O₃ WCGUUGGRBIKTOS-GPOJBZKASA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
6Q5	BindingDB: 5K3M	IC50: min: 0.75, max: 1060 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.295 (Depositor), 0.315 (DCC)
R-Value Work: 0.265 (Depositor), 0.280 (DCC)
R-Value Observed: 0.268 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.702	α = 90
b = 89.702	β = 90
c = 153.793	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
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: 2024-03-06
Changes: Data collection, Database references

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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.