Download MendeleyStructural basis for diacetylated histone H4 tail recognition by the second bromodomain of human BRD2
Padmanabhan, B., Umehara, T., Nakano, K., Jang, M.K., Ozato, K., Yokohama, S.To be published.
2E3K
Crystal structure of the human Brd2 second bromodomain in complexed with the acetylated histone H4 peptide
- PDB DOI: https://doi.org/10.2210/pdb2E3K/pdb
- Classification: TRANSCRIPTION
- Organism(s): Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2006-11-27 Released: 2007-12-11
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.268
- R-Value Work: 0.201
- R-Value Observed: 0.204
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.4 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Bromodomain-containing protein 2 | 112 | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P25440 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 15-mer peptide from Histone H4 | E [auth Q], F [auth R] | 15 | N/A | Mutation(s): 0 |  |
UniProt | |||||
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P02309 Go to UniProtKB: P02309 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P02309 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| ALY Query on ALY | E [auth Q], F [auth R] | L-PEPTIDE LINKING | C8 H16 N2 O3 |  | LYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.268
- R-Value Work: 0.201
- R-Value Observed: 0.204
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 45.828 | α = 90 |
| b = 128.591 | β = 104.7 |
| c = 45.847 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| ADSC | data collection |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2007-12-11 Deposition Author(s): Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Revision History (Full details and data files)
- Version 1.0: 2007-12-11
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.3: 2023-11-15
Changes: Data collection - Version 1.4: 2024-11-13
Changes: Structure summary
