6I80 | pdb_00006i80

Crystal Structure of the second bromodomain of BRD2 in complex with RT53

PDB DOI: https://doi.org/10.2210/pdb6I80/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-11-19 Released: 2019-11-27
Deposition Author(s): Picaud, S., Traquete, R., Bernardes, G.J.L., Newman, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Filippakopoulos, P., Structural Genomics Consortium (SGC)
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.14 Å
R-Value Free:
0.143 (Depositor), 0.157 (DCC)
R-Value Work:
0.131 (Depositor), 0.141 (DCC)
R-Value Observed:
0.131 (Depositor)

Starting Model: experimental
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Literature

Crystal Structure of the second bromodomain of BRD2 in complex with RT53

Picaud, S., Traquete, R., Bernardes, G.J.L., Newman, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Filippakopoulos, P., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 27.05 kDa
Atom Count: 2,293
Modeled Residue Count: 220
Deposited Residue Count: 220
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 2	A, B	110	Homo sapiens	Mutation(s): 0 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
H7B (Subject of Investigation/LOI) Query on H7B Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	2-[(4~{S})-6-(4-chlorophenyl)-8-methoxy-1-methyl-4~{H}-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-1-[4-(dimethylamino)piperidin-1-yl]ethanone C₂₇ H₃₁ Cl N₆ O₂ TWEGKGBKRSDRFW-QHCPKHFHSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.14 Å
R-Value Free: 0.143 (Depositor), 0.157 (DCC)
R-Value Work: 0.131 (Depositor), 0.141 (DCC)
R-Value Observed: 0.131 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.409	α = 90
b = 66.72	β = 90
c = 129.613	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-11-27

Deposition Author(s):

Bernardes, G.J.L.

Arrowsmith, C.H.

Filippakopoulos, P.

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	095751/Z/11/Z

Revision History (Full details and data files)

Version 1.0: 2019-11-27
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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