4QE8 | pdb_00004qe8

FXR with DM175 and NCoA-2 peptide

PDB DOI: https://doi.org/10.2210/pdb4QE8/pdb

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

Deposited: 2014-05-15 Released: 2015-08-12
Deposition Author(s): Kudlinzki, D., Merk, D., Linhard, V.L., Saxena, K., Sreeramulu, S., Nilsson, E., Dekker, N., Wissler, L., Bamberg, K., Schubert-Zsilavecz, M., Schwalbe, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free:
0.273 (Depositor), 0.290 (DCC)
R-Value Work:
0.249 (Depositor), 0.260 (DCC)
R-Value Observed:
0.252 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

FXR with DM175 and NCoA-2 peptide

Kudlinzki, D., Merk, D., Linhard, V.L., Saxena, K., Sreeramulu, S., Nilsson, E., Dekker, N., Wissler, L., Bamberg, K., Schubert-Zsilavecz, M., Schwalbe, H.

To be published.

Macromolecule Content

Total Structure Weight: 59.01 kDa
Atom Count: 4,101
Modelled Residue Count: 472
Deposited Residue Count: 492
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bile acid receptor	A, B	233	Homo sapiens	Mutation(s): 0 Gene Names: NR1H4, BAR, FXR, HRR1, RIP14
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 LOADING

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 2	C, D	13	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596 Go to UniProtKB: Q15596
PHAROS: Q15596 GTEx: ENSG00000140396
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15596
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
31D Query on 31D Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	E [auth A], J [auth B]	4-({2-[(4-tert-butylbenzoyl)amino]benzoyl}amino)benzoic acid C₂₅ H₂₄ N₂ O₄ JNIQPWWGQWIPLQ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] K [auth B] F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
31D	BindingDB: 4QE8	EC50: min: 280, max: 350 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free: 0.273 (Depositor), 0.290 (DCC)
R-Value Work: 0.249 (Depositor), 0.260 (DCC)
R-Value Observed: 0.252 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.483	α = 88.89
b = 48.683	β = 78.1
c = 82.201	γ = 85.07

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
autoPROC	data scaling
ABSCALE	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-08-12

Deposition Author(s):

Schubert-Zsilavecz, M.

Schwalbe, H.

Revision History (Full details and data files)

Version 1.0: 2015-08-12
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

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FXR with DM175 and NCoA-2 peptide

FXR with DM175 and NCoA-2 peptide

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

4QE8 | pdb_00004qe8