MolNFT v1 · #149322 · protein
Disulfide between E3 hect ligase SMURF2 and ubiquitin G76C
6FX4 · E3 ubiquitin-protein ligase SMURF2: “Disulfide between E3 hect ligase SMURF2 and ubiquitin G76C”. X-ray diffraction, 4 pockets (best druggability 0.69). MolNFT v1 #149322 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6FX4
- Type
- protein
- Length
- 385 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase SMURF2; Polyubiquitin-B
- EC
- 2.3.2.26
- UniProt
- Q9HAU4, P0CG47
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase SMURF2 (EC 2.3.2.26) | protein | 116 | 40% helix, 17% strand | Q9HAU4 |
| B, D | Polyubiquitin-B | protein | 76 | 24% helix, 34% strand | P0CG47 |
| C | E3 ubiquitin-protein ligase SMURF2 (EC 2.3.2.26) | protein | 117 | 39% helix, 17% strand | Q9HAU4 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.69 | 0.87 | 26 | GOL |
| 2 | 185 | 0.53 | 0.79 | 21 | empty |
| 3 | 75 | 0.49 | 0.84 | 22 | empty |
| 4 | 88 | 0.42 | 0.79 | 21 | empty |
Interfaces
5 interfaces between chains.
- C–D · 808 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 720 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 493 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 326 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 187 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6FX4 · Disulfide between E3 HECT ligase Smurf2 and Ubiquitin G76C · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HAU4 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase SMURF2 (Q9HAU4) · a predicted model of the same protein · chain A 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 Q9HAU4
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 6FX4 · PDBe 6FX4 · UniProt Q9HAU4 · UniProt P0CG47
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