Research workbench
Crystal structure of the N-terminal domain of the yeast general corepressor TUP1P
Analyse Crystal structure of the N-terminal domain of the yeast general corepressor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VP8
- Type
- protein
- Length
- 310 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- General transcriptional corepressor TUP1
- UniProt
- P16649
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 96% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | General transcriptional corepressor TUP1 | protein | 75 | 96% helix, 0% strand | P16649 |
| B | General transcriptional corepressor TUP1 | protein | 80 | 96% helix, 0% strand | P16649 |
| C | General transcriptional corepressor TUP1 | protein | 77 | 96% helix, 0% strand | P16649 |
| D | General transcriptional corepressor TUP1 | protein | 78 | 95% helix, 0% strand | P16649 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.85 | 0.91 | 63 | empty |
| 2 | 93 | 0.58 | 0.86 | 20 | empty |
| 3 | 69 | 0.58 | 0.89 | 17 | empty |
| 4 | 78 | 0.36 | 0.76 | 10 | empty |
| 5 | 53 | 0.28 | 0.74 | 11 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1704 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1695 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1103 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1090 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 774 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3VP8 · Crystal structure of the N-terminal domain of the yeast general corepressor Tup1p · the same entry in another collection · chain D against D, TM-score 1.00
- P16649 · AlphaFold monomer V2.0 prediction for general transcriptional corepressor TUP1 (P16649) · 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 P16649
- Elsewhere: RCSB PDB 3VP8 · PDBe 3VP8 · UniProt P16649
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