7E3M | pdb_00007e3m

RORgamma LBD complexed with Panaxatriol and SRC2.2

PDB DOI: https://doi.org/10.2210/pdb7E3M/pdb

Classification: IMMUNE SYSTEM/INHIBITOR
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2021-02-09 Released: 2022-03-23
Deposition Author(s): Liu, Z.H., Huang, J., Lu, W.Q., Tang, Y., Wu, Z.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.269 (Depositor), 0.199 (DCC)
R-Value Work:
0.194 (Depositor), 0.204 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of human RORgammat LBD with SRC2.2 at 2.80 Angstroms resolution

Liu, Z.H., Huang, J., Wu, Z.R., Tang, Y., Lu, W.Q.

To be published.

Macromolecule Content

Total Structure Weight: 29.81 kDa
Atom Count: 2,077
Modeled Residue Count: 251
Deposited Residue Count: 251
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor ROR-gamma	A	243	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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN	B	8	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HVL (Subject of Investigation/LOI) Query on HVL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(3R,5R,6S,8R,9R,10R,12R,13R,14R,17S)-4,4,8,10,14-pentamethyl-17-[(2R)-2,6,6-trimethyloxan-2-yl]-2,3,5,6,7,9,11,12,13,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthrene-3,6,12-triol C₃₀ H₅₂ O₄ QFJUYMMIBFBOJY-FAKBLDBGSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.269 (Depositor), 0.199 (DCC)
R-Value Work: 0.194 (Depositor), 0.204 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.446	α = 90
b = 62.446	β = 90
c = 159.766	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2022-03-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-03-23
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, 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.