MolNFT v1 · #121255 · protein
System-wide modulation of hect E3 ligases with selective ubiquitin variant probes: WWP1, ubv P2.3 and UBCH7
5HPT · NEDD4-like E3 ubiquitin-protein ligase WWP1: “System-wide modulation of hect E3 ligases with selective ubiquitin variant probes: WWP1, ubv P2.3 and UBCH7”. X-ray diffraction, 17 pockets (best druggability 0.84). MolNFT v1 #121255 on…
- PDB
- 5HPT
- Type
- protein
- Length
- 1,639 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NEDD4-like E3 ubiquitin-protein ligase WWP1; Ubiquitin variant P2.3…
- EC
- 6.3.2.-, 2.3.2.23
- UniProt
- Q9H0M0, P68036
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 7 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NEDD4-like E3 ubiquitin-protein ligase WWP1 (EC 6.3.2.-) | protein | 373 | 49% helix, 13% strand | Q9H0M0 |
| B, E | Ubiquitin variant P2.3 | protein | 76 | 20% helix, 34% strand | — |
| C | Ubiquitin-conjugating enzyme E2 L3 (EC 2.3.2.23) | protein | 151 | 33% helix, 17% strand | P68036 |
| D | NEDD4-like E3 ubiquitin-protein ligase WWP1 (EC 6.3.2.-) | protein | 371 | 47% helix, 12% strand | Q9H0M0 |
| F | Ubiquitin-conjugating enzyme E2 L3 (EC 2.3.2.23) | protein | 150 | 33% helix, 15% strand | P68036 |
| G | NEDD4-like E3 ubiquitin-protein ligase WWP1 (EC 6.3.2.-) | protein | 367 | 50% helix, 13% strand | Q9H0M0 |
| H | Ubiquitin variant P2.3 | protein | 75 | 20% helix, 33% strand | — |
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 981 | 0.84 | 0.85 | 92 | empty |
| 2 | 1170 | 0.80 | 0.81 | 124 | empty |
| 3 | 954 | 0.79 | 0.81 | 86 | empty |
| 4 | 414 | 0.75 | 0.85 | 56 | empty |
| 5 | 132 | 0.74 | 0.93 | 25 | empty |
Interfaces
11 interfaces between chains.
- A–D · 1063 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 1021 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1007 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 992 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 963 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 5HPT · System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: WWP1… · the same entry in another collection · chain H against H, TM-score 1.00
- P68036 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 L3 (P68036) · a predicted model of the same protein · chain C against A, TM-score 0.97
- Q9H0M0 · AlphaFold monomer V2.0 prediction for NEDD4-like E3 ubiquitin-protein ligase WWP1 (Q9H0M0) · a predicted model of the same protein · chain G against A, TM-score 0.96
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 Q9H0M0
- Every structure of UniProt P68036
- Elsewhere: RCSB PDB 5HPT · PDBe 5HPT · UniProt Q9H0M0 · UniProt P68036
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