Research workbench
A tandem SH2 domain in transcription elongation factor SPT6 binds the phosphorylated RNA polymerase II C-terminal repeat DOMAIN(CTD)
Analyse A tandem SH2 domain in transcription elongation factor SPT6 binds the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PJP
- Type
- protein
- Length
- 389 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription elongation factor SPT6
- UniProt
- Q6FLB1
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription elongation factor SPT6 | protein | 194 | 29% helix, 32% strand | Q6FLB1 |
| B | Transcription elongation factor SPT6 | protein | 195 | 29% helix, 31% strand | Q6FLB1 |
Ligands and binding sites
- ACT · Acetate ion · additive · 4 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.60 | 0.79 | 37 | empty |
| 2 | 149 | 0.41 | 0.74 | 18 | empty |
| 3 | 92 | 0.32 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 687 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3PJP · A Tandem SH2 Domain in Transcription Elongation Factor Spt6 Binds the Phosphorylated RNA… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6FLB1 · AlphaFold monomer V2.0 prediction for transcription elongation factor SPT6 (Q6FLB1) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q6FLB1
- Elsewhere: RCSB PDB 3PJP · PDBe 3PJP · UniProt Q6FLB1
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