Download MendeleyCrystal 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
- PDB DOI: 10.2210/pdb5ZBU/pdb
- Classification: ENDOCYTOSIS
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2018-02-12 Released: 2019-02-27
- Funding Organization(s): Wellcome Trust-DBT India Alliance
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.20 Å
- R-Value Free: 0.262
- R-Value Work: 0.214
- R-Value Observed: 0.217
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 |
| Ubiquitin-conjugating enzyme E2 D2 | B, A [auth C] | 148 | Homo sapiens | Mutation(s): 1 Gene Names: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data) |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P62837 (Homo sapiens) Explore P62837 Go to UniProtKB: P62837 | |||||
PHAROS: P62837 GTEx: ENSG00000131508 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P62837 | ||||
Protein Feature ViewExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| E3 ubiquitin-protein ligase RNF13 | C [auth A], D | 76 | Homo sapiens | Mutation(s): 0 Gene Names: RNF13, RZF EC: 2.3.2.27 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O43567 (Homo sapiens) Explore O43567 Go to UniProtKB: O43567 | |||||
PHAROS: O43567 GTEx: ENSG00000082996 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O43567 | ||||
Protein Feature ViewExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Ubiquitin | E | 76 | Homo sapiens | Mutation(s): 0 Gene Names: UBB |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47 Go to UniProtKB: P0CG47 | |||||
PHAROS: P0CG47 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0CG47 | ||||
Protein Feature ViewExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN Query on ZN | F [auth A], G [auth A], H [auth D], I [auth D] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.20 Å
- R-Value Free: 0.262
- R-Value Work: 0.214
- R-Value Observed: 0.217
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 56.559 | α = 90 |
| b = 105.74 | β = 115.49 |
| c = 60.79 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| 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 |
Revision History (Full details and data files)
- Version 1.0: 2019-02-27
Type: Initial release
