8YHS | pdb_00008yhs

The Crystal Structure of BRDT from Biortus.

PDB DOI: https://doi.org/10.2210/pdb8YHS/pdb

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

Deposited: 2024-02-28 Released: 2024-03-13
Deposition Author(s): Wang, F., Cheng, W., Lv, Z., Meng, Q., Lu, Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.222 (Depositor), 0.236 (DCC)
R-Value Work:
0.184 (Depositor), 0.195 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

The Crystal Structure of BRDT from Biortus.

Wang, F., Cheng, W., Lv, Z., Meng, Q., Lu, Y.

To be published.

Macromolecule Content

Total Structure Weight: 14.44 kDa
Atom Count: 1,103
Modeled Residue Count: 108
Deposited Residue Count: 117
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain testis-specific protein	A	117	Homo sapiens	Mutation(s): 0 Gene Names: BRDT
UniProt & NIH Common Fund Data Resources
Find proteins for Q58F21 (Homo sapiens) Explore Q58F21 Go to UniProtKB: Q58F21
PHAROS: Q58F21 GTEx: ENSG00000137948
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q58F21
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1D6J Query on A1D6J Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2,4-dimethyl-6-[6-(oxan-4-yl)-1-[(1~{S})-1-phenylethyl]imidazo[4,5-c]pyridin-2-yl]pyridazin-3-one C₂₅ H₂₇ N₅ O₂ QNFGQQDKBYVNAS-KRWDZBQOSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.222 (Depositor), 0.236 (DCC)
R-Value Work: 0.184 (Depositor), 0.195 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.567	α = 90
b = 44.38	β = 90
c = 72.125	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-03-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	China	--

Revision History (Full details and data files)

Version 1.0: 2024-03-13
Type: Initial release

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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.