Research workbench
Crystal structure of yeast SPT16 N-terminal domain
Analyse Crystal structure of yeast SPT16 N-terminal domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BIT
- Type
- protein
- Length
- 885 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fact complex subunit SPT16
- UniProt
- P32558
- Ligands
- CL
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fact complex subunit SPT16 | protein | 447 | 41% helix, 21% strand | P32558 |
| B | Fact complex subunit SPT16 | protein | 438 | 42% helix, 21% strand | P32558 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.79 | 0.83 | 82 | BME |
| 2 | 113 | 0.62 | 0.88 | 26 | CL, BME |
| 3 | 136 | 0.62 | 0.86 | 33 | CL |
| 4 | 483 | 0.60 | 0.75 | 53 | empty |
| 5 | 96 | 0.53 | 0.84 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 955 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
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 P32558
- Elsewhere: RCSB PDB 3BIT · PDBe 3BIT · UniProt P32558
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