Research workbench
Yeast TFIIA/TBP/DNA complex
Analyse Yeast TFIIA/TBP/DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YTF
- Type
- protein + DNA
- Length
- 404 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*GP*TP*AP*TP*GP*TP*AP*TP*AP*TP*AP*AP*AP*AP*C)-3'); DNA (5'…
- UniProt
- P13393, P32773, P32774
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | DNA (5'- D(*TP*GP*TP*AP*TP*GP*TP*AP*TP*AP*TP*AP*AP*AP*AP*C)-3') | dna | 16 | — | — |
| F | DNA (5'- D(*GP*TP*TP*TP*TP*AP*TP*AP*TP*AP*CP*AP*TP*AP*CP*A)-3') | dna | 16 | — | — |
| A | Protein (tata binding protein (tbp)) | protein | 180 | 27% helix, 37% strand | P13393 |
| B | Protein (transcription factor iia - TOA1N subunit) | protein | 46 | 85% helix, 0% strand | P32773 |
| C | Protein (transcription factor iia - TOA1C subunit) | protein | 46 | 0% helix, 83% strand | P32773 |
| D | Protein (transcription factor iia - TOA2 subunit) | protein | 100 | 38% helix, 40% strand | P32774 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 578 | 0.62 | 0.75 | 38 | empty |
| 2 | 63 | 0.59 | 0.90 | 16 | empty |
| 3 | 78 | 0.34 | 0.76 | 16 | empty |
Interfaces
10 interfaces between chains.
- C–D · 1724 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1094 Ų buried · 9 hydrogen bonds · protein-protein
- F–A · 839 Ų buried · 12 hydrogen bonds · protein-nucleic
- E–A · 809 Ų buried · 6 hydrogen bonds · protein-nucleic
- E–F · 709 Ų buried · 61 hydrogen bonds · nucleic-nucleic
Compared structures
- 1YTF · Yeast TFIIA/TBP/DNA complex · the same entry in another collection · chain D against D, TM-score 1.00
- P13393 · AlphaFold monomer V2.0 prediction for tata-box-binding protein (P13393) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P32773 · AlphaFold monomer V2.0 prediction for transcription initiation factor iia large subunit… · a predicted model of the same protein · chain C against A, TM-score 0.97
- P32774 · AlphaFold monomer V2.0 prediction for transcription initiation factor iia subunit 2… · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P13393
- Every structure of UniProt P32773
- Every structure of UniProt P32774
- Elsewhere: RCSB PDB 1YTF · PDBe 1YTF · UniProt P13393 · UniProt P32773 · UniProt P32774
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