5DKD: Bromodomain of human BRG1

Crystal structure of the bromodomain of human BRG1 (SMARCA4) in complex with PFI-3 chemical probe. Determined by X-ray diffraction at 2.0 Å resolution. Released 14 Oct 2015.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,002
Mol. weight: 29.61 kDa
Ligands: 5BW, ZN
Released: 14 Oct 2015

Explore 5DKD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DKD contains 16 α-helices and 4 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A and B: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1458-1471	14
β-strand	1473	1	1
β-strand	1480	1	1
α-helix	1483-1485	3
α-helix	1488-1490	3
α-helix	1495-1500	6
α-helix	1507-1515	9
α-helix	1522-1539	18
α-helix	1541	1
α-helix	1545-1565	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription activator BRG1	A, B	protein	121	Homo sapiens	P51532 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5DKD_1 Transcription activator BRG1 (chains A, B)
SMLSPNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFK
KIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKED
D

Ligands and cofactors

ID	Name	Formula	Copies
5BW	(2E)-1-(2-hydroxyphenyl)-3-[(1R,4R)-5-(pyridin-2-yl)-2,5-diazabicyclo[2.2.1]hep…	C19 H19 N3 O2	2
ZN	Zinc ion	Zn	2

Water and common crystallization additives (EDO) are not listed.

Primary citation

Crystal structure of the bromodomain of human BRG1 (SMARCA4) in complex with PFI-3 chemical probe. Tallant, C., Owen, D.R., Gerstenberger, B.S. et al. To be published.

Other PDB entries of the same protein (UniProt P51532 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7TAB 1.16 Å, G-925 bound to the SMARCA4 (BRG1) Bromodomain
2GRC 1.5 Å, 1.5 A structure of bromodomain from human BRG1 protein, a central ATPase of SWI/SNF…
6ZS2 1.57 Å, Crystal Structure of the bromodomain of human transcription activator BRG1 (SMARCA4) in…
7TD9 1.61 Å, G-059 bound to the SMARCA4 (BRG1) Bromodomain
6HR2 1.76 Å, Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA4 and…
3UVD 1.85 Å, Crystal Structure of the bromodomain of human Transcription activator BRG1 (SMARCA4) in…
5EA1 2.0 Å, Crystal Structure of SMARCA4 bromodomain in complex with MPD
9DTX 2.11 Å, Crystal structure of PRT3789 in complex with the bromodomain of human BRG1 (SMARCA4) and…
7VRB 2.39 Å, Structure of the Human BRG1/SS18 complex
9UXC 2.74 Å, The ADP-bound structure of BCL7B-containing ARP module of the human SWI/SNF complex
7VDT 2.8 Å, The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex
9WBZ 2.9 Å, The structure of NCP-motor-ARP module of ncBAF-nucleosome complex

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