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), 0.252 (DCC)
R-Value Work:
0.217 (Depositor), 0.218 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: experimental
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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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	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), 0.252 (DCC)
R-Value Work: 0.217 (Depositor), 0.218 (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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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

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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.