Research workbench
Cryo-EM structure of the human saga coactivator complex (trrap, core)
Analyse Cryo-EM structure of the human saga coactivator complex (trrap, core) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KTR
- Type
- protein
- Length
- 5,168 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRANSFORMATION/TRANSCRIPTION domain-associated protein, TRANSFORMATION/TRANSCRIPTION…
- UniProt
- F2Z2U4, O75529, Q8NEM7, O94864, Q9HBM6, Q9Y6J9, Q16514, Q12962, O75486, Q96BN2, O15265
- Ligands
- IHP
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 11 distinct chains · 57% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRANSFORMATION/TRANSCRIPTION domain-associated protein, TRANSFORMATION/TRANSCRIPTION domain-associated protein, TRANSFORMATION/TRANSCRIPTION domain-associated protein, TRANSFORMATION/TRANSCRIPTION domain-associated protein | protein | 3042 | 67% helix, 3% strand | F2Z2U4 |
| B | TAF5-like RNA polymerase II P300/CBP-associated factor- associated factor 65 kda subunit 5L | protein | 534 | 21% helix, 32% strand | O75529 |
| C | Isoform 3 of transcription factor SPT20 homolog | protein | 407 | 37% helix, 15% strand | Q8NEM7 |
| D | Staga complex 65 subunit GAMMA,DHAA,STAGA complex 65 subunit GAMMA,STAGA complex 65 subunit GAMMA,DHAA,STAGA complex 65 subunit GAMMA,STAGA complex 65 subunit GAMMA,DHAA | protein | 219 | 58% helix, 1% strand | O94864 |
| E | Transcription initiation factor tfiid subunit 9B | protein | 124 | 53% helix, 2% strand | Q9HBM6 |
| F | TAF6-like RNA polymerase II P300/CBP-associated factor- associated factor 65 kda subunit 6L | protein | 130 | 41% helix, 15% strand | Q9Y6J9 |
| G | Transcription initiation factor tfiid subunit 12 | protein | 103 | 61% helix, 2% strand | Q16514 |
| H | Transcription initiation factor tfiid subunit 10 | protein | 99 | 54% helix, 3% strand | Q12962 |
| I | Transcription initiation protein SPT3 HOMOLOG,TRANSCRIPTION initiation protein SPT3 HOMOLOG,TRANSCRIPTION initiation protein SPT3 homolog | protein | 243 | 64% helix, 1% strand | O75486 |
| J | Transcriptional adapter 1 | protein | 214 | 49% helix, 3% strand | Q96BN2 |
| N | Ataxin-7 | protein | 53 | 32% helix, 11% strand | O15265 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 887 | 0.89 | 0.92 | 112 | empty |
| 2 | 1084 | 0.88 | 0.89 | 131 | empty |
| 3 | 1124 | 0.88 | 0.89 | 130 | empty |
| 4 | 1117 | 0.86 | 0.87 | 101 | empty |
| 5 | 1084 | 0.86 | 0.86 | 81 | empty |
Interfaces
43 interfaces between chains.
- B–C · 5408 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 4738 Ų buried · 40 hydrogen bonds · protein-protein
- D–H · 3110 Ų buried · 17 hydrogen bonds · protein-protein
- G–J · 2491 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 2382 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7KTR · Cryo-EM structure of the human SAGA coactivator complex (TRRAP, core) · the same entry in another collection · chain N against N, TM-score 1.00
- Q9Y6J9 · AlphaFold monomer V2.0 prediction for TAF6-like RNA polymerase II P300/CBP-associated… · a predicted model of the same protein · chain F against A, TM-score 0.90
- O94864 · AlphaFold monomer V2.0 prediction for staga complex 65 subunit gamma (O94864) · a predicted model of the same protein · chain D against A, TM-score 0.85
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 F2Z2U4
- Every structure of UniProt O75529
- Every structure of UniProt Q8NEM7
- Every structure of UniProt O94864
- Every structure of UniProt Q9HBM6
- Every structure of UniProt Q9Y6J9
- Every structure of UniProt Q16514
- Every structure of UniProt Q12962
- Every structure of UniProt O75486
- Every structure of UniProt Q96BN2
- Every structure of UniProt O15265
- Elsewhere: RCSB PDB 7KTR · PDBe 7KTR · UniProt F2Z2U4 · UniProt O75529 · UniProt Q8NEM7 · UniProt O94864 · UniProt Q9HBM6 · UniProt Q9Y6J9 · UniProt Q16514 · UniProt Q12962 · UniProt O75486 · UniProt Q96BN2 · UniProt O15265
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