Research workbench
Structure of yeast UBR1 in complex with UBC2 and monoubiquitinated N- degron
Analyse Structure of yeast UBR1 in complex with UBC2 and monoubiquitinated N- degron in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MEY
- Type
- protein
- Length
- 2,033 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase UBR1; Ubiquitin; Ubiquitin-conjugating enzyme E2 2…
- EC
- 2.3.2.27, 2.3.2.23
- UniProt
- P19812, P0CG47, P06104
- Ligands
- Z3V, ZN
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase UBR1 (EC 2.3.2.27) | protein | 1731 | 52% helix, 7% strand | P19812 |
| C | Ubiquitin | protein | 71 | 23% helix, 32% strand | P0CG47 |
| B | Ubiquitin-conjugating enzyme E2 2 (EC 2.3.2.23) | protein | 153 | 33% helix, 16% strand | P06104 |
| D | Ubiquitin | protein | 75 | 23% helix, 29% strand | P0CG47 |
| F | Monoubiquitinated N-degron | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- Z3V · 2-(ethylamino)ethane-1-thiol · ligand · chains C, B, D
- 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.82 | 0.97 | 23 | empty |
| 2 | 1181 | 0.79 | 0.81 | 141 | empty |
| 3 | 675 | 0.77 | 0.82 | 55 | empty |
| 4 | 817 | 0.75 | 0.79 | 86 | empty |
| 5 | 746 | 0.75 | 0.80 | 68 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1574 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1047 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 508 Ų buried · 10 hydrogen bonds · protein-protein
- C–B · 484 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 444 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7MEY · Structure of yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron · the same entry in another collection · chain C against C, TM-score 1.00
- 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
- 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 0.93
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 P19812
- Every structure of UniProt P0CG47
- Every structure of UniProt P06104
- Elsewhere: RCSB PDB 7MEY · PDBe 7MEY · UniProt P19812 · UniProt P0CG47 · UniProt P06104
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