Research workbench
Crystal structure of the STH1 bromodomain from saccharomyces cerevisiae at 2.2 ångström resolution
Analyse Crystal structure of the STH1 bromodomain from saccharomyces cerevisiae at 2.2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UY1
- Type
- protein
- Length
- 881 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear protein STH1/NPS1
- EC
- 3.6.4.12
- UniProt
- P32597
- Ligands
- MG
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 61% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear protein STH1/NPS1 (EC 3.6.4.12) | protein | 110 | 62% helix, 2% strand | P32597 |
| B, D, G | Nuclear protein STH1/NPS1 (EC 3.6.4.12) | protein | 111 | 61% helix, 2% strand | P32597 |
| C, H | Nuclear protein STH1/NPS1 (EC 3.6.4.12) | protein | 110 | 61% helix, 2% strand | P32597 |
| E | Nuclear protein STH1/NPS1 (EC 3.6.4.12) | protein | 109 | 60% helix, 2% strand | P32597 |
| F | Nuclear protein STH1/NPS1 (EC 3.6.4.12) | protein | 109 | 61% helix, 2% strand | P32597 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.86 | 0.95 | 59 | empty |
| 2 | 272 | 0.84 | 0.95 | 41 | empty |
| 3 | 260 | 0.84 | 0.95 | 42 | empty |
| 4 | 255 | 0.83 | 0.95 | 42 | empty |
| 5 | 105 | 0.40 | 0.76 | 16 | empty |
Interfaces
12 interfaces between chains.
- E–G · 1061 Ų buried · 13 hydrogen bonds · protein-protein
- F–H · 1051 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1047 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1019 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 300 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 modified (engineered).
Compared structures
- 6UY1 · Crystal structure of the Sth1 bromodomain from Saccharomyces cerevisiae at 2.2 Angstrom… · the same entry in another collection · chain H against H, TM-score 1.00
- P32597 · AlphaFold monomer V2.0 prediction for nuclear protein STH1/NPS1 (P32597) · a predicted model of the same protein · chain F 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 P32597
- Elsewhere: RCSB PDB 6UY1 · PDBe 6UY1 · UniProt P32597
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