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Download EndnoteCrystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub
Sarkar, S., Datta, A.B.To be published.
5ZBU
Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub
- DOI: 10.2210/pdb5ZBU/pdb
- Classification: ENDOCYTOSIS
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): 1
- Deposited: 2018-02-12 Released: 2019-02-27
- Funding Organization(s): Wellcome Trust-DBT India Alliance
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.2 Å
- R-Value Free: 0.262
- R-Value Work: 0.214
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: Sequence | Structure
Entity ID: 1 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| Ubiquitin-conjugating enzyme E2 D2 | C, B | 148 | Homo sapiens | Mutation(s): 1 Gene Names: UBE2D2 (PUBC1, UBC4, UBC5B, UBCH4, UBCH5B) EC: 2.3.2.23 |
Find proteins for P62837 (Homo sapiens) Go to Gene View: UBE2D2 Go to UniProtKB: P62837 | ||||
Entity ID: 2 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| E3 ubiquitin-protein ligase RNF13 | A, D | 76 | Homo sapiens | Mutation(s): 0 Gene Names: RNF13 (RZF) EC: 2.3.2.27 |
Find proteins for O43567 (Homo sapiens) Go to Gene View: RNF13 Go to UniProtKB: O43567 | ||||
Entity ID: 3 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| Ubiquitin | E | 76 | Homo sapiens | Mutation(s): 0 Gene Names: UBB |
Find proteins for P0CG47 (Homo sapiens) Go to Gene View: UBB Go to UniProtKB: P0CG47 | ||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN Query on ZN | A, D | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.2 Å
- R-Value Free: 0.262
- R-Value Work: 0.214
- Space Group: P 1 21 1
Unit Cell:
| Length (Å) | Angle (°) |
|---|---|
| a = 56.559 | α = 90.00 |
| b = 105.740 | β = 115.49 |
| c = 60.790 | γ = 90.00 |
| Software Name | Purpose |
|---|---|
| XDS | data reduction |
| Aimless | data scaling |
| PHENIX | refinement |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Deposited Date: 2018-02-12
- Released Date: 2019-02-27
- Deposition Author(s): Datta, A.B., Sarkar, S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Wellcome Trust-DBT India Alliance | India | 500241/Z/11/Z |
