Research workbench
Saga TRA1 module
Analyse Saga TRA1 module in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T9J
- Type
- protein
- Length
- 3,617 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor SPT20; Transcription initiation factor tfiid subunit 12…
- UniProt
- P50875, Q03761, P38811
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 57% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Transcription factor SPT20 | protein | 43 | 49% helix, 0% strand | P50875 |
| I | Transcription initiation factor tfiid subunit 12 | protein | 61 | 0% helix, 3% strand | Q03761 |
| T | Transcription-associated protein 1 | protein | 3513 | 58% helix, 2% strand | P38811 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1173 | 0.87 | 0.88 | 123 | empty |
| 2 | 1157 | 0.84 | 0.85 | 129 | empty |
| 3 | 605 | 0.83 | 0.88 | 82 | empty |
| 4 | 860 | 0.81 | 0.83 | 75 | empty |
| 5 | 148 | 0.79 | 0.95 | 24 | empty |
Interfaces
3 interfaces between chains.
- I–T · 2943 Ų buried · 24 hydrogen bonds · protein-protein
- B–T · 1847 Ų buried · 16 hydrogen bonds · protein-protein
- B–I · 759 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6T9J · SAGA Tra1 module · the same entry in another collection · chain B against B, TM-score 1.00
- P50875 · AlphaFold monomer V2.0 prediction for transcription factor SPT20 (P50875) · a predicted model of the same protein · chain B against A, TM-score 0.38
- Q03761 · AlphaFold monomer V2.0 prediction for transcription initiation factor tfiid subunit 12… · a predicted model of the same protein · chain I against A, TM-score 0.28
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 P50875
- Every structure of UniProt Q03761
- Every structure of UniProt P38811
- Elsewhere: RCSB PDB 6T9J · PDBe 6T9J · UniProt P50875 · UniProt Q03761 · UniProt P38811
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