5HEM | pdb_00005hem

Crystal structure of the N-terminus D161Y bromodomain mutant of human BRD2

PDB DOI: https://doi.org/10.2210/pdb5HEM/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-01-06 Released: 2016-01-20
Deposition Author(s): Tallant, C., Lori, C., Pasquo, A., Chiaraluce, R., Consalvi, V., Newman, J.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.199 (Depositor), 0.206 (DCC)
R-Value Work:
0.167 (Depositor), 0.180 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the N-terminus D161Y bromodomain mutant of human BRD2

Tallant, C., Lori, C., Pasquo, A., Chiaraluce, R., Consalvi, V., Newman, J.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 30.38 kDa
Atom Count: 2,225
Modeled Residue Count: 237
Deposited Residue Count: 252
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 2	A, B	126	Homo sapiens	Mutation(s): 1 Gene Names: BRD2, KIAA9001, RING3
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens) Explore P25440 Go to UniProtKB: P25440
PHAROS: P25440 GTEx: ENSG00000204256
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25440
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	H [auth A], J [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain J [auth B] Interactions & Density Focus chain H [auth A] Focus chain J [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.199 (Depositor), 0.206 (DCC)
R-Value Work: 0.167 (Depositor), 0.180 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.73	α = 90
b = 68.73	β = 90
c = 113.364	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-01-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-01-20
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description