3LYI

PWWP Domain of Human Bromodomain-Containing Protein 1

PDB DOI: https://doi.org/10.2210/pdb3LYI/pdb

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

Deposited: 2010-02-26 Released: 2010-03-16
Deposition Author(s): Lam, R., Zeng, H., Ni, S., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Wu, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.276
R-Value Work: 0.234
R-Value Observed: 0.236

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structural and histone binding ability characterizations of human PWWP domains.

Wu, H., Zeng, H., Lam, R., Tempel, W., Amaya, M.F., Xu, C., Dombrovski, L., Qiu, W., Wang, Y., Min, J.

(2011) PLoS One 6: e18919-e18919

PubMed: 21720545 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0018919
Primary Citation of Related Structures:
3EAE, 3L42, 3LLR, 3LYI, 3MO8, 3PFS, 3PMI, 3QBY, 3QJ6, 3QKJ

PubMed Abstract:
The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently.

Organizational Affiliation

Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.

Macromolecule Content

Total Structure Weight: 28.79 kDa
Atom Count: 1,880
Modelled Residue Count: 225
Deposited Residue Count: 252
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 1	A, B	126	Homo sapiens	Mutation(s): 0 Gene Names: BRD1, BRL, BRPF2
UniProt & NIH Common Fund Data Resources
Find proteins for O95696 (Homo sapiens) Explore O95696 Go to UniProtKB: O95696
PHAROS: O95696 GTEx: ENSG00000100425
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O95696
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OCS Query on OCS Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	CYSTEINESULFONIC ACID C₃ H₇ N O₅ S XVOYSCVBGLVSOL-REOHCLBHSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.276
R-Value Work: 0.234
R-Value Observed: 0.236
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.029	α = 90
b = 46.085	β = 90
c = 130.712	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MxDC	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-03-16

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2010-03-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-03-21
Changes: Database references
Version 1.3: 2017-11-08
Changes: Refinement description
Version 1.4: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2023-11-22
Changes: Data collection