MolNFT v1 · #75515 · protein
Crystal structure of the SPT6 tandem SH2 domain from saccharomyces cerevisiae, form native SPT6 (1247-1451)
3PSK · Transcription elongation factor SPT6: “Crystal structure of the SPT6 tandem SH2 domain from saccharomyces cerevisiae, form native SPT6 (1247-1451)”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 3PSK
- Type
- protein
- Length
- 766 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription elongation factor SPT6
- UniProt
- P23615
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transcription elongation factor SPT6 | protein | 199 | 26% helix, 31% strand | P23615 |
| C | Transcription elongation factor SPT6 | protein | 185 | 26% helix, 32% strand | P23615 |
| D | Transcription elongation factor SPT6 | protein | 183 | 28% helix, 32% strand | P23615 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.81 | 0.85 | 87 | empty |
| 2 | 468 | 0.73 | 0.82 | 51 | empty |
| 3 | 202 | 0.49 | 0.75 | 24 | empty |
| 4 | 244 | 0.45 | 0.72 | 32 | empty |
| 5 | 106 | 0.43 | 0.77 | 16 | empty |
Interfaces
5 interfaces between chains.
- B–C · 776 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 588 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 579 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 537 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 257 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3PSK · Crystal Structure of the Spt6 Tandem SH2 Domain from Saccharomyces cerevisiae, Form… · the same entry in another collection · chain A against A, TM-score 1.00
- P23615 · AlphaFold monomer V2.0 prediction for transcription elongation factor SPT6 (P23615) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P23615
- Elsewhere: RCSB PDB 3PSK · PDBe 3PSK · UniProt P23615
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