5EWW

Crystal structure of the human BRPF1 bromodomain in complex with SEED21

PDB DOI: https://doi.org/10.2210/pdb5EWW/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-11-21 Released: 2016-11-02
Deposition Author(s): Zhu, J., Wiedmer, L., Caflisch, A.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.210
R-Value Work: 0.186
R-Value Observed: 0.187

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Crystal structure of the human BRPF1 bromodomain in complex with SEED21

Zhu, J., Wiedmer, L., Caflisch, A.

To be published.

Macromolecule Content

Total Structure Weight: 14.02 kDa
Atom Count: 1,079
Modelled Residue Count: 113
Deposited Residue Count: 116
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peregrin	A	116	Homo sapiens	Mutation(s): 0 Gene Names: BRPF1, BR140
UniProt & NIH Common Fund Data Resources
Find proteins for P55201 (Homo sapiens) Explore P55201 Go to UniProtKB: P55201
PHAROS: P55201 GTEx: ENSG00000156983
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P55201
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5SK Query on 5SK Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	~{N}-[(2~{R})-butan-2-yl]-1-methyl-[1,2,4]triazolo[4,3-a]quinoxalin-4-amine C₁₄ H₁₇ N₅ NPOOPJOEQAWGNZ-SECBINFHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.210
R-Value Work: 0.186
R-Value Observed: 0.187
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.52	α = 90
b = 60.52	β = 90
c = 62.92	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-11-02

Deposition Author(s):

Zhu, J.

Wiedmer, L.

Caflisch, A.

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History (Full details and data files)

Version 1.0: 2016-11-02
Type: Initial release
Version 2.0: 2024-01-10
Changes: Atomic model, Data collection, Database references, Refinement description

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5EWW

Crystal structure of the human BRPF1 bromodomain in complex with SEED21

Crystal structure of the human BRPF1 bromodomain in complex with SEED21

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)