6JNR | pdb_00006jnr

RXRa structure complexed with CU-6PMN and SRC1 peptide.

PDB DOI: https://doi.org/10.2210/pdb6JNR/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-03-18 Released: 2020-03-25
Deposition Author(s): Kawasaki, M., Nakano, S., Motoyama, T., Yamada, S., Watanabe, M., Takamura, Y., Fujihara, M., Tokiwa, H., Kakuta, H., Ito, S.
Funding Organization(s): Japan Society for the Promotion of Science

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.238 (Depositor), 0.250 (DCC)
R-Value Work:
0.179 (Depositor), 0.190 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

RXRa structure complexed with CU-6PMN and SRC1 peptide.

Kawasaki, M., Nakano, S., Motoyama, T., Yamada, S., Watanabe, M., Takamura, Y., Fujihara, M., Tokiwa, H., Kakuta, H., Ito, S.

To be published.

Macromolecule Content

Total Structure Weight: 57.93 kDa
Atom Count: 3,709
Modelled Residue Count: 448
Deposited Residue Count: 510
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoic acid receptor RXR-alpha	A, B	243	Homo sapiens	Mutation(s): 0 Gene Names: RXRA, NR2B1
UniProt & NIH Common Fund Data Resources
Find proteins for P19793 (Homo sapiens) Explore P19793 Go to UniProtKB: P19793
PHAROS: P19793 GTEx: ENSG00000186350
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19793
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN	C, D	12	Homo sapiens	Mutation(s): 0 EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788 Go to UniProtKB: Q15788
PHAROS: Q15788 GTEx: ENSG00000084676
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15788
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WY5 (Subject of Investigation/LOI) Query on WY5 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B]	E [auth A], F [auth B]	7-oxidanyl-2-oxidanylidene-6-(3,5,5,8,8-pentamethyl-6,7-dihydronaphthalen-2-yl)chromene-3-carboxylic acid C₂₅ H₂₆ O₅ UYPOSIGCFZMVDD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
WY5	BindingDB: 6JNR	Ki: 230 (nM) from 1 assay(s)
		Kd: min: 233, max: 1.32e+4 (nM) from 3 assay(s)
		EC50: 22 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.238 (Depositor), 0.250 (DCC)
R-Value Work: 0.179 (Depositor), 0.190 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.39	α = 90
b = 64.39	β = 90
c = 111.168	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-03-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	16K18688
Japan Society for the Promotion of Science	Japan	18K14391
Japan Society for the Promotion of Science	Japan	12J06716