2YYN | pdb_00002yyn

Crystal structure of human bromodomain protein

PDB DOI: https://doi.org/10.2210/pdb2YYN/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2007-04-30 Released: 2008-05-06
Deposition Author(s): Kishishita, S., Uchikubo-Kamo, T., Murayama, K., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.285 (Depositor), 0.292 (DCC)
R-Value Work:
0.239 (Depositor), 0.246 (DCC)
R-Value Observed:
0.239 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2YYN

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of human bromodomain protein

Kishishita, S., Uchikubo-Kamo, T., Murayama, K., Terada, T., Shirouzu, M., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 61.95 kDa
Atom Count: 3,896
Modeled Residue Count: 453
Deposited Residue Count: 540
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription intermediary factor 1-alpha	A, B, C, D	135	Homo sapiens	Mutation(s): 0 Gene Names: TRIM24, RNF82, TIF1, TIF1A EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for O15164 (Homo sapiens) Explore O15164 Go to UniProtKB: O15164
PHAROS: O15164 GTEx: ENSG00000122779
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15164
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.285 (Depositor), 0.292 (DCC)
R-Value Work: 0.239 (Depositor), 0.246 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.855	α = 90
b = 76.16	β = 90
c = 107.599	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-05-06

Deposition Author(s):

Uchikubo-Kamo, T.

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2008-05-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2020-09-09
Changes: Database references, Structure summary
Version 1.3: 2022-12-21
Changes: Database references
Version 1.4: 2024-11-13
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.