Research workbench
Structure of yeast UBR1 in complex with UBC2 and N-degron
Analyse Structure of yeast UBR1 in complex with UBC2 and N-degron in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MEX
- Type
- protein
- Length
- 1,967 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; Ubiquitin-conjugating enzyme E2 2; N-degron; E3 ubiquitin-protein ligase UBR1
- EC
- 2.3.2.23, 2.3.2.27
- UniProt
- P0CG48, P06104, P19812
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Ubiquitin | protein | 76 | 20% helix, 34% strand | P0CG48 |
| B | Ubiquitin-conjugating enzyme E2 2 (EC 2.3.2.23) | protein | 150 | 34% helix, 18% strand | P06104 |
| D | N-degron | protein | 4 | 0% helix, 0% strand | — |
| A | E3 ubiquitin-protein ligase UBR1 (EC 2.3.2.27) | protein | 1737 | 51% helix, 7% strand | P19812 |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.81 | 0.82 | 113 | empty |
| 2 | 114 | 0.79 | 0.97 | 21 | empty |
| 3 | 991 | 0.77 | 0.79 | 92 | empty |
| 4 | 821 | 0.74 | 0.79 | 81 | empty |
| 5 | 588 | 0.67 | 0.77 | 56 | empty |
Interfaces
6 interfaces between chains.
- B–A · 2026 Ų buried · 12 hydrogen bonds · protein-protein
- C–B · 1002 Ų buried · 14 hydrogen bonds · protein-protein
- C–A · 740 Ų buried · 7 hydrogen bonds · protein-protein
- D–A · 405 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 128 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 7MEX · Structure of yeast Ubr1 in complex with Ubc2 and N-degron · the same entry in another collection · chain C against C, TM-score 1.00
- P06104 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 2 (P06104) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P19812 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase UBR1 (P19812) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P0CG48
- Every structure of UniProt P06104
- Every structure of UniProt P19812
- Elsewhere: RCSB PDB 7MEX · PDBe 7MEX · UniProt P0CG48 · UniProt P06104 · UniProt P19812
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