MolNFT v1 · #74059 · protein
Structure and function of a ubiquitin binding site within the catalytic domain of a hect ubiquitin ligase
3OLM · E3 ubiquitin-protein ligase RSP5: “Structure and function of a ubiquitin binding site within the catalytic domain of a hect ubiquitin ligase”. X-ray diffraction, 5 pockets (best druggability 0.74). MolNFT v1 #74059 on GenesisL1: 3D…
- PDB
- 3OLM
- Type
- protein
- Length
- 486 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RSP5; Ubiquitin
- EC
- 6.3.2.-
- UniProt
- P39940, P0CG63
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase RSP5 (EC 6.3.2.-) | protein | 412 | 44% helix, 14% strand | P39940 |
| D | Ubiquitin | protein | 74 | 16% helix, 31% strand | P0CG63 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.74 | 0.80 | 66 | empty |
| 2 | 239 | 0.54 | 0.77 | 33 | empty |
| 3 | 92 | 0.35 | 0.74 | 12 | empty |
| 4 | 80 | 0.30 | 0.73 | 14 | empty |
| 5 | 50 | 0.27 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–D · 899 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3OLM · Structure and Function of a Ubiquitin Binding Site within the Catalytic Domain of a HECT… · the same entry in another collection · chain A against A, TM-score 1.00
- P0CG63 · AlphaFold monomer V2.0 prediction for polyubiquitin (P0CG63) · a predicted model of the same protein · chain D against A, TM-score 0.96
- P39940 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RSP5 (P39940) · a predicted model of the same protein · chain A against A, TM-score 0.65
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 P39940
- Every structure of UniProt P0CG63
- Elsewhere: RCSB PDB 3OLM · PDBe 3OLM · UniProt P39940 · UniProt P0CG63
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