MolNFT v1 · #121247 · protein
System-wide modulation of hect E3 ligases with selective ubiquitin variant probes: RSP5 and ubv R5.4
5HPL: “System-wide modulation of hect E3 ligases with selective ubiquitin variant probes: RSP5 and ubv R5.4”. X-ray diffraction, 13 pockets (best druggability 0.72). MolNFT v1 #121247 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5HPL
- Type
- protein
- Length
- 902 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RSP5; Ubiquitin variant R5.4
- UniProt
- P39940
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RSP5 | protein | 370 | 49% helix, 15% strand | P39940 |
| B | RSP5 | protein | 370 | 49% helix, 15% strand | P39940 |
| C, D | Ubiquitin variant R5.4 | protein | 81 | 22% helix, 35% strand | — |
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.72 | 0.83 | 30 | empty |
| 2 | 865 | 0.71 | 0.76 | 88 | empty |
| 3 | 955 | 0.71 | 0.75 | 61 | empty |
| 4 | 307 | 0.62 | 0.80 | 26 | empty |
| 5 | 382 | 0.62 | 0.78 | 34 | empty |
Interfaces
5 interfaces between chains.
- B–D · 965 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 944 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 508 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 343 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 277 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5HPL · System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: Rsp5… · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.98
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
- Elsewhere: RCSB PDB 5HPL · PDBe 5HPL · UniProt P39940
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