Download MendeleyCrystal structure of human DPPA3 in complex with human UHRF1 PHD domain
Shiraishi, N., Arita, K.To be published.
8WMS
Crystal structure of human DPPA3 in complex with human UHRF1 PHD domain
- PDB DOI: https://doi.org/10.2210/pdb8WMS/pdb
- Classification: GENE REGULATION
- Organism(s): Homo sapiens
- Expression System: unidentified plasmid
- Mutation(s): No
- Deposited: 2023-10-04 Released: 2024-07-31
- Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.266
- R-Value Work: 0.233
- R-Value Observed: 0.235
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 1.0 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 |
| E3 ubiquitin-protein ligase UHRF1 | 68 | Homo sapiens | Mutation(s): 0 Gene Names: UHRF1, ICBP90, NP95, RNF106 EC: 2.3.2.27 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q96T88 (Homo sapiens) Explore Q96T88 Go to UniProtKB: Q96T88 | |||||
PHAROS: Q96T88 GTEx: ENSG00000276043 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q96T88 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Developmental pluripotency-associated protein 3 | 38 | Homo sapiens | Mutation(s): 0 Gene Names: DPPA3, STELLAR |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q6W0C5 (Homo sapiens) Explore Q6W0C5 Go to UniProtKB: Q6W0C5 | |||||
PHAROS: Q6W0C5 GTEx: ENSG00000187569 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q6W0C5 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN (Subject of Investigation/LOI) Query on ZN | C [auth A], D [auth A], E [auth A], F [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.266
- R-Value Work: 0.233
- R-Value Observed: 0.235
- Space Group: I 41 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 77.802 | α = 90 |
| b = 77.802 | β = 90 |
| c = 140.674 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-07-31 Deposition Author(s): Shiraishi, N., Arita, K.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Japan Society for the Promotion of Science (JSPS) | Japan | JP18H02392, |
| Japan Society for the Promotion of Science (JSPS) | Japan | JP19H05741 |
| Japan Society for the Promotion of Science (JSPS) | Japan | JP19H05294 |
| Japan Science and Technology | Japan | 14530337 |
Revision History (Full details and data files)
- Version 1.0: 2024-07-31
Type: Initial release
