Research workbench
Structure of the tpr domain of SGT2 in complex with yeast SSA1 peptide fragment
Analyse Structure of the tpr domain of SGT2 in complex with yeast SSA1 peptide fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LYN
- Type
- protein
- Length
- 280 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small glutamine-rich tetratricopeptide repeat-containing protein 2…
- UniProt
- Q12118
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Small glutamine-rich tetratricopeptide repeat-containing protein 2 | protein | 133 | 83% helix, 0% strand | Q12118 |
| C, D | Pro-thr-val-glu-glu-val-asp | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.52 | 0.76 | 31 | empty |
Interfaces
5 interfaces between chains.
- A–D · 540 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 498 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 420 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5LYN · Structure of the Tpr Domain of Sgt2 in complex with yeast Ssa1 peptide fragment · the same entry in another collection · chain A against A, TM-score 1.00
- Q12118 · AlphaFold monomer V2.0 prediction for small glutamine-rich tetratricopeptide… · a predicted model of the same protein · chain A against A, TM-score 0.97
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
- Elsewhere: RCSB PDB 5LYN · PDBe 5LYN · UniProt Q12118
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