7AMH | pdb_00007amh

SmBRD3(2), Second Bromodomain of Bromodomain 3 from Schistosoma mansoni in complex with DM-A-33, an iBET726 analogue

PDB DOI: https://doi.org/10.2210/pdb7AMH/pdb

Classification: PROTEIN BINDING
Organism(s): Schistosoma mansoni
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-10-08 Released: 2021-10-20
Deposition Author(s): McArdle, D., Schiedel, M., McDonough, M.A., Conway, S.J.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.251 (Depositor), 0.250 (DCC)
R-Value Work:
0.217 (Depositor), 0.220 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

SBM3_2, Second Bromodomain of Bromodomain 3 from Schistosoma mansoni in complex with DM1, an iBET726 analogue

McArdle, D.J.B., Schiedel, M., McDonough, M.A., Conway, S.J.

To be published.

Macromolecule Content

Total Structure Weight: 30.97 kDa
Atom Count: 2,170
Modeled Residue Count: 226
Deposited Residue Count: 258
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative bromodomain-containing protein 3, brd3	A, B	129	Schistosoma mansoni	Mutation(s): 0
UniProt
Find proteins for A0A5K4ESD7 (Schistosoma mansoni) Explore A0A5K4ESD7 Go to UniProtKB: A0A5K4ESD7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5K4ESD7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RN5 (Subject of Investigation/LOI) Query on RN5 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]	4-{(2S, 4R)-1-acetyl-4-[(1-benzothiophen-6-yl)amino]-2-methyl-1,2,3,4-tetrahydroquinolin-6-yl}benzoic acid C₂₇ H₂₄ N₂ O₃ S PSXHCEJOKMTHEO-UPCLLVRISA-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: 1.86 Å
R-Value Free: 0.251 (Depositor), 0.250 (DCC)
R-Value Work: 0.217 (Depositor), 0.220 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.201	α = 90
b = 84.111	β = 90
c = 126.736	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-10-20

Deposition Author(s):

McDonough, M.A.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/S507015/1

Revision History (Full details and data files)

Version 1.0: 2021-10-20
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

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.