Research workbench
Structure of saga bound to tbp, including SPT8 and dub
Analyse Structure of saga bound to tbp, including SPT8 and dub in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TBM
- Type
- protein
- Length
- 6,481 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tata-box binding protein (tbp); Transcriptional coactivator HFI1/ADA1; Subunit of saga…
- EC
- 3.4.19.12
- UniProt
- C4QZA3, C4QZ39, C4QZ05, C4R3E4, C4R5C7, C4QXP2, C4R150, C4R4L4, C4QW33, C4QZS5, C4QYV4, C4R2A4, J3QS39, C4QY61, C4R2D9, C4R1P1
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 18 distinct chains · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | Tata-box binding protein (tbp) | protein | 180 | 24% helix, 33% strand | — |
| A | Transcriptional coactivator HFI1/ADA1 | protein | 173 | 47% helix, 1% strand | C4QZA3 |
| C | Subunit of saga histone acetyltransferase complex | protein | 95 | 34% helix, 9% strand | C4QZ39 |
| F | SPT20 | protein | 210 | 29% helix, 11% strand | C4QZ05 |
| D | Subunit of the saga and saga-like transcriptional regulatory complexes, interacts with SPT15P to act | protein | 209 | 61% helix, 0% strand | C4R3E4 |
| E | Subunit of the saga transcriptional regulatory complex, involved in proper assembly of the complex | protein | 154 | 72% helix, 0% strand | C4R5C7 |
| J | Transcription initiation factor tfiid subunit 10 | protein | 96 | 54% helix, 0% strand | C4QXP2 |
| K | Subunit (61/68 kda) of tfiid and saga complexes | protein | 154 | 33% helix, 2% strand | C4R150 |
| G | Subunit (90 kda) of tfiid and saga complexes | protein | 522 | 22% helix, 26% strand | C4R4L4 |
| H | Subunit (60 kda) of tfiid and saga complexes | protein | 421 | 50% helix, 1% strand | C4QW33 |
| I | Subunit (17 kda) of tfiid and saga complexes, involved in RNA polymerase II transcription initiation | protein | 123 | 48% helix, 1% strand | C4QZS5 |
| L | Transcription-associated protein | protein | 2968 | 58% helix, 2% strand | C4QYV4 |
| B | Transcriptional regulator involved in glucose repression of GAL4P-regulated genes | protein | 76 | 68% helix, 0% strand | C4R2A4 |
| N | SPT8 | protein | 335 | 1% helix, 39% strand | — |
| R | Polyubiquitin-B | protein | 76 | 24% helix, 32% strand | J3QS39 |
| Q | Ubiquitin carboxyl-terminal hydrolase (EC 3.4.19.12) | protein | 482 | 32% helix, 22% strand | C4QY61 |
| O | Saga-associated factor 11 | protein | 117 | 38% helix, 9% strand | C4R2D9 |
| P | Transcription and mRNA export factor SUS1 | protein | 90 | 81% helix, 0% strand | C4R1P1 |
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 | 1086 | 0.87 | 0.88 | 87 | empty |
| 2 | 756 | 0.86 | 0.89 | 66 | empty |
| 3 | 602 | 0.85 | 0.90 | 78 | empty |
| 4 | 914 | 0.84 | 0.86 | 113 | empty |
| 5 | 1026 | 0.83 | 0.84 | 85 | empty |
Interfaces
49 interfaces between chains.
- G–H · 3802 Ų buried · 56 hydrogen bonds · protein-protein
- F–G · 2905 Ų buried · 20 hydrogen bonds · protein-protein
- Q–O · 2525 Ų buried · 88 hydrogen bonds · protein-protein
- K–L · 2431 Ų buried · 23 hydrogen bonds · protein-protein
- A–K · 2397 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 6TBM · Structure of SAGA bound to TBP, including Spt8 and DUB · the same entry in another collection · chain M against M, TM-score 1.00
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 C4QZA3
- Every structure of UniProt C4QZ39
- Every structure of UniProt C4QZ05
- Every structure of UniProt C4R3E4
- Every structure of UniProt C4R5C7
- Every structure of UniProt C4QXP2
- Every structure of UniProt C4R150
- Every structure of UniProt C4R4L4
- Every structure of UniProt C4QW33
- Every structure of UniProt C4QZS5
- Every structure of UniProt C4QYV4
- Every structure of UniProt C4R2A4
- Every structure of UniProt J3QS39
- Every structure of UniProt C4QY61
- Every structure of UniProt C4R2D9
- Every structure of UniProt C4R1P1
- Elsewhere: RCSB PDB 6TBM · PDBe 6TBM · UniProt C4QZA3 · UniProt C4QZ39 · UniProt C4QZ05 · UniProt C4R3E4 · UniProt C4R5C7 · UniProt C4QXP2 · UniProt C4R150 · UniProt C4R4L4 · UniProt C4QW33 · UniProt C4QZS5 · UniProt C4QYV4 · UniProt C4R2A4 · UniProt J3QS39 · UniProt C4QY61 · UniProt C4R2D9 · UniProt C4R1P1
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