8F6G | pdb_00008f6g

Crystal structure of BPTF bromodomain in complex with BZ2

PDB DOI: https://doi.org/10.2210/pdb8F6G/pdb

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

Deposited: 2022-11-16 Released: 2024-05-22
Deposition Author(s): Nithianantham, S., Fischer, M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.226 (Depositor), 0.230 (DCC)
R-Value Work:
0.191 (Depositor), 0.190 (DCC)
R-Value Observed:
0.193 (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 BPTF bromodomain in complex with BZ2

Nithianantham, S., Fischer, M.

To be published.

Macromolecule Content

Total Structure Weight: 14.73 kDa
Atom Count: 1,164
Modeled Residue Count: 121
Deposited Residue Count: 123
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleosome-remodeling factor subunit BPTF	A	123	Homo sapiens	Mutation(s): 0 Gene Names: BPTF, FAC1, FALZ
UniProt & NIH Common Fund Data Resources
Find proteins for Q12830 (Homo sapiens) Explore Q12830 Go to UniProtKB: Q12830
PHAROS: Q12830 GTEx: ENSG00000171634
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12830
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XHK (Subject of Investigation/LOI) Query on XHK 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]	6-[4-(2-aminoethyl)anilino]-5-chloro-3-methylpyrimidin-4(3H)-one C₁₃ H₁₅ Cl N₄ O SGIPWPOFBZCITE-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.226 (Depositor), 0.230 (DCC)
R-Value Work: 0.191 (Depositor), 0.190 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.976	α = 90
b = 66.859	β = 104.94
c = 39.564	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-22

Deposition Author(s):

Nithianantham, S.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R35GM142772-01

Revision History (Full details and data files)

Version 1.0: 2024-05-22
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.