Download MendeleyStructure of wild-type human MBD4 bound to a G:T mismatch
Ouzon-Shubeita, H., Lin, Y.-L., Lee, S.To be published.
5CHZ
Structure of wild-type human MBD4 bound to a G:T mismatch
- PDB DOI: https://doi.org/10.2210/pdb5CHZ/pdb
- NAKB: 5CHZ
- Classification: HYDROLASE/DNA
- Organism(s): Homo sapiens, synthetic construct
- Expression System: Escherichia coli BL21
- Mutation(s): No
- Deposited: 2015-07-10 Released: 2016-07-20
- Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS), Welch Foundation
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.83 Å
- R-Value Free: 0.209
- R-Value Work: 0.174
- R-Value Observed: 0.175
wwPDB Validation 3D Report Full Report
This is version 1.3 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 |
| Methyl-CpG-binding domain protein 4 | 192 | Homo sapiens | Mutation(s): 0 Gene Names: MBD4, MED1 EC: 3.2.2 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O95243 (Homo sapiens) Explore O95243 Go to UniProtKB: O95243 | |||||
PHAROS: O95243 GTEx: ENSG00000129071 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O95243 | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| 7-mer DNA | B [auth C] | 7 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| 12-mer DNA(G) | C [auth D] | 12 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| 5-mer DNA | D [auth B] | 5 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MG Query on MG | E [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.83 Å
- R-Value Free: 0.209
- R-Value Work: 0.174
- R-Value Observed: 0.175
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 41.886 | α = 90 |
| b = 54.875 | β = 90 |
| c = 104.522 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| MOLREP | phasing |
| HKL-2000 | data scaling |
| HKL-2000 | data reduction |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-07-20 Deposition Author(s): Ouzon-Shubeita, H., Lin, Y.-L., Lee, S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) | United States | R21ES023101 |
| Welch Foundation | United States | F-1741 |
Revision History (Full details and data files)
- Version 1.0: 2016-07-20
Type: Initial release - Version 1.1: 2017-09-27
Changes: Author supporting evidence, Derived calculations - Version 1.2: 2019-12-18
Changes: Author supporting evidence - Version 1.3: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
