Research workbench
Crystal structure of the SGT2 N domain and the GET5 ubl domain complex
Analyse Crystal structure of the SGT2 N domain and the GET5 ubl domain complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZDM
- Type
- protein
- Length
- 396 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small glutamine-rich tetratricopeptide repeat- containing protein 2; Ubiquitin-like…
- UniProt
- Q12118, Q12285
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Small glutamine-rich tetratricopeptide repeat- containing protein 2 | protein | 69 | 80% helix, 0% strand | Q12118 |
| B, E | Small glutamine-rich tetratricopeptide repeat- containing protein 2 | protein | 50 | 70% helix, 0% strand | Q12118 |
| C, F | Ubiquitin-like protein MDY2 | protein | 79 | 22% helix, 37% strand | Q12285 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.68 | 0.85 | 25 | empty |
| 2 | 64 | 0.33 | 0.76 | 18 | empty |
| 3 | 66 | 0.30 | 0.74 | 11 | empty |
| 4 | 62 | 0.29 | 0.74 | 12 | empty |
Interfaces
9 interfaces between chains.
- D–E · 763 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 763 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 761 Ų buried · 0 hydrogen bonds · protein-protein
- E–F · 383 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 380 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3ZDM · Crystal structure of the Sgt2 N domain and the Get5 UBL domain complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q12118 · AlphaFold monomer V2.0 prediction for small glutamine-rich tetratricopeptide… · a predicted model of the same protein · chain B against A, TM-score 0.94
- Q12285 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein MDY2 (Q12285) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 Q12118
- Every structure of UniProt Q12285
- Elsewhere: RCSB PDB 3ZDM · PDBe 3ZDM · UniProt Q12118 · UniProt Q12285
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