Research workbench
TRIM25 RING domain in complex with Ubc13-Ub conjugate
Analyse TRIM25 RING domain in complex with Ubc13-Ub conjugate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EYA
- Type
- protein
- Length
- 612 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Homo sapiens
- Molecule
- Ubiquitin-conjugating enzyme E2 N; Tripartite motif-containing 25 variant; Polyubiquitin-B
- EC
- 2.3.2.23
- UniProt
- P61088, Q59GW5, P0CG47
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · resolution 2.4 · 4 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23) | protein | 149 | 35% helix, 21% strand | P61088 |
| F | Tripartite motif-containing 25 variant | protein | 76 | 37% helix, 17% strand | Q59GW5 |
| G | Tripartite motif-containing 25 variant | protein | 86 | 33% helix, 15% strand | Q59GW5 |
| C, D | Polyubiquitin-B | protein | 76 | 20% helix, 34% strand | P0CG47 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.70 | 0.98 | 19 | empty |
| 2 | 92 | 0.51 | 0.83 | 22 | empty |
| 3 | 98 | 0.42 | 0.78 | 18 | empty |
| 4 | 83 | 0.41 | 0.79 | 19 | empty |
| 5 | 145 | 0.40 | 0.74 | 25 | empty |
Interfaces
9 interfaces between chains.
- A–D · 972 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 952 Ų buried · 16 hydrogen bonds · protein-protein
- F–G · 909 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 599 Ų buried · 7 hydrogen bonds · protein-protein
- G–B · 550 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- 5EYA · TRIM25 ring domain in complex with UBC13-ub conjugate · the same entry in another collection · chain G against G, TM-score 1.00
- P61088 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 N (P61088) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P0CG47 · AlphaFold monomer V2.0 prediction for polyubiquitin-B (P0CG47) · a predicted model of the same protein · chain C against A, TM-score 0.91
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P61088
- Every structure of UniProt Q59GW5
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5EYA · PDBe 5EYA · UniProt P61088 · UniProt Q59GW5 · UniProt P0CG47
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.