Research workbench
Structure of active gid E3 ubiquitin ligase complex minus GID2 and delta GID9 ring domain
Analyse Structure of active gid E3 ubiquitin ligase complex minus GID2 and delta GID9… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SWY
- Type
- protein
- Length
- 2,030 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar import and degradation protein 28; Glucose-induced degradation protein 8…
- EC
- 2.3.2.27
- UniProt
- P40547, P40208, P53076, P38263, P40492
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 5 | Vacuolar import and degradation protein 28 | protein | 789 | 66% helix, 1% strand | P40547 |
| 8 | Glucose-induced degradation protein 8 | protein | 325 | 57% helix, 3% strand | P40208 |
| 1 | Vacuolar import and degradation protein 30,VACUOLAR import and degradation protein 30,VACUOLAR import and degradation protein 30,VACUOLAR import and degradation protein 30,VACUOLAR import and degradation protein 30,VACUOLAR import and degradation protein 30, vacuolar import and degradation protein 30,VACUOLAR import and degradation protein 30,VACUOLAR import and degradation protein 30, vacuolar import and degradation protein 30,VACUOLAR import and degradation protein 30,VACUOLAR import and degra | protein | 542 | 44% helix, 14% strand | P53076 |
| 4 | Vacuolar import and degradation protein 24 | protein | 217 | 13% helix, 31% strand | P38263 |
| 9 | Protein FYV10,PROTEIN FYV10,PROTEIN FYV10,PROTEIN FYV10, protein FYV10,PROTEIN FYV10,PROTEIN FYV10 (EC 2.3.2.27) | protein | 157 | 63% helix, 1% strand | P40492 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.85 | 0.86 | 98 | empty |
| 2 | 1123 | 0.84 | 0.85 | 89 | empty |
| 3 | 778 | 0.75 | 0.80 | 76 | empty |
| 4 | 547 | 0.71 | 0.80 | 68 | empty |
| 5 | 551 | 0.71 | 0.80 | 49 | empty |
Interfaces
7 interfaces between chains.
- 8–1 · 4749 Ų buried · 47 hydrogen bonds · protein-protein
- 5–8 · 4421 Ų buried · 35 hydrogen bonds · protein-protein
- 5–4 · 3223 Ų buried · 36 hydrogen bonds · protein-protein
- 5–1 · 2422 Ų buried · 17 hydrogen bonds · protein-protein
- 8–9 · 1372 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6SWY · Structure of active GID E3 ubiquitin ligase complex minus Gid2 and delta Gid9 RING domain · the same entry in another collection · chain 9 against 9, TM-score 1.00
- P40547 · AlphaFold monomer V2.0 prediction for vacuolar import and degradation protein 28 (P40547) · a predicted model of the same protein · chain 5 against A, TM-score 1.00
- P38263 · AlphaFold monomer V2.0 prediction for vacuolar import and degradation protein 24 (P38263) · a predicted model of the same protein · chain 4 against A, TM-score 0.87
- P40208 · AlphaFold monomer V2.0 prediction for glucose-induced degradation protein 8 (P40208) · a predicted model of the same protein · chain 8 against A, TM-score 0.69
- P40492 · AlphaFold monomer V2.0 prediction for protein FYV10 (P40492) · a predicted model of the same protein · chain 9 against A, TM-score 0.65
- P53076 · AlphaFold monomer V2.0 prediction for vacuolar import and degradation protein 30 (P53076) · a predicted model of the same protein · chain 1 against A, TM-score 0.57
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 P40547
- Every structure of UniProt P40208
- Every structure of UniProt P53076
- Every structure of UniProt P38263
- Every structure of UniProt P40492
- Elsewhere: RCSB PDB 6SWY · PDBe 6SWY · UniProt P40547 · UniProt P40208 · UniProt P53076 · UniProt P38263 · UniProt P40492
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.