5DKC | pdb_00005dkc

Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with PFI-3 chemical probe

PDB DOI: https://doi.org/10.2210/pdb5DKC/pdb

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

Deposited: 2015-09-03 Released: 2015-10-14
Deposition Author(s): Tallant, C., Owen, D.R., Gerstenberger, B.S., Fedorov, O., Savitsky, P., Nunez-Alonso, G., Fonseca, M., Krojer, T., Filippakopoulos, P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Muller, S., Knapp, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.211 (Depositor), 0.218 (DCC)
R-Value Work:
0.194 (Depositor), 0.201 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with PFI-3 chemical probe

Tallant, C., Owen, D.R., Gerstenberger, B.S., Fedorov, O., Savitsky, P., Nunez-Alonso, G., Fonseca, M., Krojer, T., Filippakopoulos, P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Muller, S., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 14.77 kDa
Atom Count: 1,047
Modeled Residue Count: 110
Deposited Residue Count: 123
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable global transcription activator SNF2L2	A	123	Homo sapiens	Mutation(s): 0 Gene Names: SMARCA2, BAF190B, BRM, SNF2A, SNF2L2 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P51531 (Homo sapiens) Explore P51531 Go to UniProtKB: P51531
PHAROS: P51531 GTEx: ENSG00000080503
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P51531
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5BW Query on 5BW 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]	(2E)-1-(2-hydroxyphenyl)-3-[(1R,4R)-5-(pyridin-2-yl)-2,5-diazabicyclo[2.2.1]hept-2-yl]prop-2-en-1-one C₁₉ H₁₉ N₃ O₂ INAICWLVUAKEPB-QSTFCLMHSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
5BW	BindingDB: 5DKC	Kd: min: 18, max: 9.70e+4 (nM) from 6 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.211 (Depositor), 0.218 (DCC)
R-Value Work: 0.194 (Depositor), 0.201 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.424	α = 90
b = 74.424	β = 90
c = 89.856	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-10-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-10-14
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description