8HD3 | pdb_00008hd3

Farnesoid X Receptor Agonists_FXR fused with a HD3 peptide

PDB DOI: https://doi.org/10.2210/pdb8HD3/pdb

Classification: NUCLEAR PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-11-03 Released: 2023-11-08
Deposition Author(s): Lu, X., Zhang, H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.251 (Depositor), 0.260 (DCC)
R-Value Work:
0.205 (Depositor), 0.220 (DCC)
R-Value Observed:
0.208 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of FXR fused with a HD3 peptide in complex with agonist QT0127

Lu, X., Zhang, H.

To be published.

Macromolecule Content

Total Structure Weight: 60.68 kDa
Atom Count: 4,054
Modeled Residue Count: 491
Deposited Residue Count: 520
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesoid X Receptor	A, B	260	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RI1 (Homo sapiens) Explore Q96RI1 Go to UniProtKB: Q96RI1
PHAROS: Q96RI1 GTEx: ENSG00000012504
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96RI1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XAW (Subject of Investigation/LOI) Query on XAW 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]	[(3s,5s,7s)-adamantan-1-yl][4-(2-amino-5-chlorophenyl)piperazin-1-yl]methanone C₂₁ H₂₈ Cl N₃ O SNWNZTLWPJKTEO-OFIQSVQDSA-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: 2.29 Å
R-Value Free: 0.251 (Depositor), 0.260 (DCC)
R-Value Work: 0.205 (Depositor), 0.220 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.032	α = 90
b = 34.408	β = 91.324
c = 110.83	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-11-08
Type: Initial release

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.