Research workbench
Gid subcomplex: GID12 bound substrate receptor scaffolding module
Analyse Gid subcomplex: GID12 bound substrate receptor scaffolding module in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WUG
- Type
- protein
- Length
- 2,239 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…
- UniProt
- P40547, P40208, A0A6L0ZCH7, A0A6A5Q1W0, A0A6A5Q188
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 5 | Vacuolar import and degradation protein 28 | protein | 782 | 67% helix, 1% strand | P40547 |
| 8 | Glucose-induced degradation protein 8 | protein | 317 | 62% helix, 3% strand | P40208 |
| 1 | Vacuolar import and degradation protein 30 | protein | 402 | 36% helix, 19% strand | A0A6L0ZCH7 |
| 4 | Vacuolar import and degradation protein 24 | protein | 230 | 13% helix, 30% strand | A0A6A5Q1W0 |
| Y | HLJ1_G0042170.MRNA.1.CDS.1 | protein | 508 | 14% helix, 38% strand | A0A6A5Q188 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1145 | 0.87 | 0.88 | 94 | empty |
| 2 | 1083 | 0.84 | 0.84 | 117 | empty |
| 3 | 956 | 0.83 | 0.84 | 85 | empty |
| 4 | 874 | 0.73 | 0.77 | 98 | empty |
| 5 | 1188 | 0.73 | 0.76 | 116 | empty |
Interfaces
7 interfaces between chains.
- 8–1 · 4272 Ų buried · 41 hydrogen bonds · protein-protein
- 5–8 · 3638 Ų buried · 35 hydrogen bonds · protein-protein
- 5–4 · 3300 Ų buried · 37 hydrogen bonds · protein-protein
- 5–1 · 2062 Ų buried · 12 hydrogen bonds · protein-protein
- 4–Y · 1583 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7WUG · GID subcomplex: Gid12 bound Substrate Receptor Scaffolding module · the same entry in another collection · chain 8 against 8, 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 0.98
- 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 0.71
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 A0A6L0ZCH7
- Every structure of UniProt A0A6A5Q1W0
- Every structure of UniProt A0A6A5Q188
- Elsewhere: RCSB PDB 7WUG · PDBe 7WUG · UniProt P40547 · UniProt P40208 · UniProt A0A6L0ZCH7 · UniProt A0A6A5Q1W0 · UniProt A0A6A5Q188
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