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), 0.262 (DCC)
R-Value Work:
0.205 (Depositor), 0.219 (DCC)
R-Value Observed:
0.208 (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

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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	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]

Binding Affinity Annotations
ID	Source	Binding Affinity
XAW	BindingDB: 8HD3	EC50: min: 1040, max: 1050 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.251 (Depositor), 0.262 (DCC)
R-Value Work: 0.205 (Depositor), 0.219 (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

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Ligand Structure Quality Assessment

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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
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

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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.