MolNFT v1 · #183502 · protein
Supramolecular assembly module of yeast chelator-gid SR4 E3 ubiquitin ligase
7NSB · Vacuolar import and degradation protein 30: “Supramolecular assembly module of yeast chelator-gid SR4 E3 ubiquitin ligase”. Electron microscopy, 20 pockets (best druggability 0.82). MolNFT v1 #183502 on GenesisL1: 3D structure…
- PDB
- 7NSB
- Type
- protein
- Length
- 1,775 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar import and degradation protein 30; Glucose-induced degradation protein 7…
- UniProt
- P53076, P25569, P40208
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a | Vacuolar import and degradation protein 30 | protein | 568 | 43% helix, 12% strand | P53076 |
| g | Glucose-induced degradation protein 7 | protein | 429 | 10% helix, 30% strand | P25569 |
| 7 | Glucose-induced degradation protein 7 | protein | 531 | 27% helix, 23% strand | P25569 |
| h | Glucose-induced degradation protein 8 | protein | 247 | 58% helix, 0% strand | P40208 |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 500 | 0.82 | 0.89 | 38 | empty |
| 2 | 467 | 0.82 | 0.89 | 36 | empty |
| 3 | 895 | 0.79 | 0.82 | 82 | empty |
| 4 | 550 | 0.69 | 0.78 | 52 | empty |
| 5 | 663 | 0.68 | 0.77 | 67 | empty |
Interfaces
4 interfaces between chains.
- a–h · 4721 Ų buried · 28 hydrogen bonds · protein-protein
- g–7 · 2039 Ų buried · 11 hydrogen bonds · protein-protein
- a–7 · 1704 Ų buried · 8 hydrogen bonds · protein-protein
- a–g · 663 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7NSB · Supramolecular assembly module of yeast Chelator-GID SR4 E3 ubiquitin ligase · the same entry in another collection · chain h against h, TM-score 1.00
- P25569 · AlphaFold monomer V2.0 prediction for glucose-induced degradation protein 7 (P25569) · a predicted model of the same protein · chain g against A, TM-score 0.81
- P40208 · AlphaFold monomer V2.0 prediction for glucose-induced degradation protein 8 (P40208) · a predicted model of the same protein · chain h against A, TM-score 0.79
- P53076 · AlphaFold monomer V2.0 prediction for vacuolar import and degradation protein 30 (P53076) · a predicted model of the same protein · chain a against A, TM-score 0.61
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 P53076
- Every structure of UniProt P25569
- Every structure of UniProt P40208
- Elsewhere: RCSB PDB 7NSB · PDBe 7NSB · UniProt P53076 · UniProt P25569 · UniProt P40208
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