MolNFT v1 · #177374 · protein + DNA
Scp promoter-bound tfiid-tfiia in post tbp-loading state
7EGJ · Transcription initiation factor tfiid subunit 1: “Scp promoter-bound tfiid-tfiia in post tbp-loading state”. Electron microscopy, 20 pockets (best druggability 0.87). MolNFT v1 #177374 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7EGJ
- Type
- protein + DNA
- Length
- 5,635 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription initiation factor tfiid subunit 1; Transcription initiation factor tfiid…
- EC
- 2.3.1.48, 2.7.11.1
- UniProt
- P21675, Q6P1X5, O00268, Q15542, P49848, Q15545, Q7Z7C8, Q16594, Q12962, Q16514, P52657, P20226, P52655, Q5VWG9, Q15544, Q15543
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 24 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription initiation factor tfiid subunit 1 (EC 2.3.1.48, 2.7.11.1) | protein | 620 | 38% helix, 13% strand | P21675 |
| B | Transcription initiation factor tfiid subunit 2 | protein | 963 | 40% helix, 20% strand | Q6P1X5 |
| D | Transcription initiation factor tfiid subunit 4 | protein | 196 | 62% helix, 3% strand | O00268 |
| E | Transcription initiation factor tfiid subunit 5 | protein | 547 | 24% helix, 30% strand | Q15542 |
| F | Transcription initiation factor tfiid subunit 6 | protein | 412 | 56% helix, 3% strand | P49848 |
| G | Transcription initiation factor tfiid subunit 7 | protein | 144 | 26% helix, 38% strand | Q15545 |
| H | Transcription initiation factor tfiid subunit 8 | protein | 209 | 45% helix, 2% strand | Q7Z7C8 |
| I | Transcription initiation factor tfiid subunit 9 | protein | 120 | 51% helix, 4% strand | Q16594 |
| J | Transcription initiation factor tfiid subunit 10 | protein | 90 | 58% helix, 3% strand | Q12962 |
| L | Transcription initiation factor tfiid subunit 12 | protein | 76 | 64% helix, 4% strand | Q16514 |
| O | Transcription initiation factor iia subunit 2 | protein | 97 | 36% helix, 34% strand | P52657 |
| P | Tata-box-binding protein | protein | 177 | 27% helix, 38% strand | P20226 |
| Q | Transcription initiation factor iia subunit 1 | protein | 101 | 43% helix, 37% strand | P52655 |
| X | DNA (74-mer) | dna | 74 | — | — |
| Y | DNA (74-mer) | dna | 74 | — | — |
| c | Transcription initiation factor tfiid subunit 3 | protein | 127 | 53% helix, 3% strand | Q5VWG9 |
| d | Transcription initiation factor tfiid subunit 4 | protein | 158 | 58% helix, 4% strand | O00268 |
| e | Transcription initiation factor tfiid subunit 5 | protein | 539 | 19% helix, 26% strand | Q15542 |
| f | Transcription initiation factor tfiid subunit 6 | protein | 403 | 55% helix, 4% strand | P49848 |
| i | Transcription initiation factor tfiid subunit 9 | protein | 121 | 45% helix, 3% strand | Q16594 |
| j | Transcription initiation factor tfiid subunit 10 | protein | 95 | 55% helix, 3% strand | Q12962 |
| k | Transcription initiation factor tfiid subunit 11 | protein | 98 | 63% helix, 0% strand | Q15544 |
| l | Transcription initiation factor tfiid subunit 12 | protein | 107 | 57% helix, 3% strand | Q16514 |
| m | Transcription initiation factor tfiid subunit 13 | protein | 87 | 69% helix, 1% strand | Q15543 |
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 | 963 | 0.87 | 0.88 | 109 | empty |
| 2 | 1061 | 0.86 | 0.87 | 99 | empty |
| 3 | 1159 | 0.85 | 0.86 | 111 | empty |
| 4 | 331 | 0.84 | 0.94 | 41 | empty |
| 5 | 881 | 0.83 | 0.85 | 92 | empty |
Interfaces
74 interfaces between chains.
- A–G · 5055 Ų buried · 82 hydrogen bonds · protein-protein
- X–Y · 3399 Ų buried · 325 hydrogen bonds · nucleic-nucleic
- O–Q · 2660 Ų buried · 30 hydrogen bonds · protein-protein
- c–j · 2639 Ų buried · 13 hydrogen bonds · protein-protein
- F–H · 2630 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- Q6P1X5 · AlphaFold monomer V2.0 prediction for transcription initiation factor tfiid subunit 2… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P20226 · AlphaFold monomer V2.0 prediction for tata-box-binding protein (P20226) · a predicted model of the same protein · chain P against A, TM-score 0.98
- P52657 · AlphaFold monomer V2.0 prediction for transcription initiation factor iia subunit 2… · a predicted model of the same protein · chain O against A, TM-score 0.96
- Q15542 · AlphaFold monomer V2.0 prediction for transcription initiation factor tfiid subunit 5… · a predicted model of the same protein · chain E against A, TM-score 0.94
- Q16514 · AlphaFold monomer V2.0 prediction for transcription initiation factor tfiid subunit 12… · a predicted model of the same protein · chain L against A, TM-score 0.94
- Q15543 · AlphaFold monomer V2.0 prediction for transcription initiation factor tfiid subunit 13… · a predicted model of the same protein · chain m against A, TM-score 0.91
- Q15544 · AlphaFold monomer V2.0 prediction for transcription initiation factor tfiid subunit 11… · a predicted model of the same protein · chain k against A, TM-score 0.90
- Q12962 · AlphaFold monomer V2.0 prediction for transcription initiation factor tfiid subunit 10… · a predicted model of the same protein · chain J against A, TM-score 0.89
- P52655 · AlphaFold monomer V2.0 prediction for transcription initiation factor iia subunit 1… · a predicted model of the same protein · chain Q against A, TM-score 0.88
- Q16594 · AlphaFold monomer V2.0 prediction for transcription initiation factor tfiid subunit 9… · a predicted model of the same protein · chain I against A, TM-score 0.87
- Q5VWG9 · AlphaFold monomer V2.0 prediction for transcription initiation factor tfiid subunit 3… · a predicted model of the same protein · chain c against A, TM-score 0.86
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 P21675
- Every structure of UniProt Q6P1X5
- Every structure of UniProt O00268
- Every structure of UniProt Q15542
- Every structure of UniProt P49848
- Every structure of UniProt Q15545
- Every structure of UniProt Q7Z7C8
- Every structure of UniProt Q16594
- Every structure of UniProt Q12962
- Every structure of UniProt Q16514
- Every structure of UniProt P52657
- Every structure of UniProt P20226
- Every structure of UniProt P52655
- Every structure of UniProt Q5VWG9
- Every structure of UniProt Q15544
- Every structure of UniProt Q15543
- Elsewhere: RCSB PDB 7EGJ · PDBe 7EGJ · UniProt P21675 · UniProt Q6P1X5 · UniProt O00268 · UniProt Q15542 · UniProt P49848 · UniProt Q15545 · UniProt Q7Z7C8 · UniProt Q16594 · UniProt Q12962 · UniProt Q16514 · UniProt P52657 · UniProt P20226 · UniProt P52655 · UniProt Q5VWG9 · UniProt Q15544 · UniProt Q15543
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