Download MendeleyUncovering the Bromodomain Interactome using Site-Specific Azide-Acetyllysine Photochemistry, Proteomic Profiling and Structural Characterization
Wagner, S., Fedorov, E., Sudhamalla, B., Jnawali, H.N., Debiec, R., Ghosh, A., Islam, K.(2021) bioRxiv
7RJO
Crystal structure of human Bromodomain containing protein 4 (BRD4) in complex with hnRNPK
- PDB DOI: https://doi.org/10.2210/pdb7RJO/pdb
- Classification: SIGNALING PROTEIN
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2021-07-21 Released: 2022-08-03
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.38 Å
- R-Value Free: 0.198 (Depositor), 0.200 (DCC)
- R-Value Work: 0.176 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.177 (Depositor)
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 2.1 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Bromodomain-containing protein 4 | 127 | Homo sapiens | Mutation(s): 0 Gene Names: BRD4, HUNK1 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O60885 (Homo sapiens) Explore O60885 Go to UniProtKB: O60885 | |||||
PHAROS: O60885 GTEx: ENSG00000141867 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O60885 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Heterogeneous nuclear ribonucleoprotein K | 10 | Homo sapiens | Mutation(s): 0 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P61978 (Homo sapiens) Explore P61978 Go to UniProtKB: P61978 | |||||
PHAROS: P61978 GTEx: ENSG00000165119 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P61978 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | D [auth A], E [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | F [auth A], G [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| NA Query on NA | C [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| ALY Query on ALY | B | L-PEPTIDE LINKING | C8 H16 N2 O3 |  | LYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.38 Å
- R-Value Free: 0.198 (Depositor), 0.200 (DCC)
- R-Value Work: 0.176 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.177 (Depositor)
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 48.454 | α = 90 |
| b = 52.08 | β = 90 |
| c = 53.325 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
| PDB_EXTRACT | data extraction |
Entry History & Funding Information
Deposition Data
- Released Date: 2022-08-03 Deposition Author(s): Fedorov, E., Islam, K., Ghosh, A.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | R01GM123234 |
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | R01GM130752 |
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | P01GM118303 |
Revision History (Full details and data files)
- Version 1.0: 2022-08-03
Type: Initial release - Version 1.1: 2022-08-24
Changes: Database references - Version 1.2: 2023-10-18
Changes: Data collection, Database references, Refinement description - Version 2.0: 2023-11-15
Changes: Atomic model, Data collection - Version 2.1: 2024-10-16
Changes: Structure summary
