Research workbench
Structure of human tfiid-iia bound to core promoter DNA
Analyse Structure of human tfiid-iia bound to core promoter DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FUR
- Type
- protein + DNA
- Length
- 2,412 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tata-box-binding protein; Transcription initiation factor iia subunit 1; Transcription…
- EC
- 2.3.1.48, 2.7.11.1
- UniProt
- P20226, P52655, P52657, P21675, Q15545, Q6P1X5, P49848, Q7Z7C8
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 12 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tata-box-binding protein | protein | 180 | 26% helix, 39% strand | P20226 |
| B | Transcription initiation factor iia subunit 1 | protein | 43 | 88% helix, 0% strand | P52655 |
| C | Transcription initiation factor iia subunit 1 | protein | 47 | 0% helix, 81% strand | P52655 |
| D | Transcription initiation factor iia subunit 2 | protein | 97 | 41% helix, 39% strand | P52657 |
| E | Super core promoter | dna | 80 | — | — |
| F | Super core promoter | dna | 80 | — | — |
| G | Transcription initiation factor tfiid subunit 1 (EC 2.3.1.48, 2.7.11.1) | protein | 406 | 34% helix, 19% strand | P21675 |
| H | Transcription initiation factor tfiid subunit 7 | protein | 123 | 20% helix, 42% strand | Q15545 |
| I | Transcription initiation factor tfiid subunit 2 | protein | 912 | 37% helix, 18% strand | Q6P1X5 |
| J | Transcription initiation factor tfiid subunit 6 | protein | 220 | 80% helix, 0% strand | P49848 |
| K | Transcription initiation factor tfiid subunit 6 | protein | 198 | 78% helix, 0% strand | P49848 |
| L | Transcription initiation factor tfiid subunit 8 | protein | 26 | 92% helix, 0% strand | Q7Z7C8 |
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 | 1068 | 0.84 | 0.85 | 116 | empty |
| 2 | 917 | 0.78 | 0.80 | 94 | empty |
| 3 | 397 | 0.75 | 0.85 | 56 | empty |
| 4 | 1036 | 0.73 | 0.77 | 84 | empty |
| 5 | 373 | 0.72 | 0.84 | 51 | empty |
Interfaces
21 interfaces between chains.
- G–H · 4053 Ų buried · 79 hydrogen bonds · protein-protein
- E–F · 3751 Ų buried · 398 hydrogen bonds · nucleic-nucleic
- C–D · 1685 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1009 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 860 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified, 1 isopeptide (phosphorylation, isopeptide).
Compared structures
- 5FUR · Structure of human TFIID-IIA bound to core promoter DNA · the same entry in another collection · chain L against L, 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 P20226
- Every structure of UniProt P52655
- Every structure of UniProt P52657
- Every structure of UniProt P21675
- Every structure of UniProt Q15545
- Every structure of UniProt Q6P1X5
- Every structure of UniProt P49848
- Every structure of UniProt Q7Z7C8
- Elsewhere: RCSB PDB 5FUR · PDBe 5FUR · UniProt P20226 · UniProt P52655 · UniProt P52657 · UniProt P21675 · UniProt Q15545 · UniProt Q6P1X5 · UniProt P49848 · UniProt Q7Z7C8
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