MolNFT v1 · #25350 · protein + DNA
Tfiib (human core DOMAIN)/TBP (A.THALIANA)/TATA element ternary complex
1VOL · DNA (5'-D(*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*TP*G)…: “Tfiib (human core DOMAIN)/TBP (A.THALIANA)/TATA element ternary complex”. X-ray diffraction, 4 pockets (best druggability 0.65). MolNFT v1 #25350 on GenesisL1: 3D…
- PDB
- 1VOL
- Type
- protein + DNA
- Length
- 423 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*TP*G)- 3'); DNA…
- UniProt
- Q00403, P28147
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'-D(*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*TP*G)- 3') | dna | 16 | — | — |
| D | DNA (5'-D(*CP*AP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*C)- 3') | dna | 16 | — | — |
| A | Protein (transcription factor iib (tfiib)) | protein | 204 | 65% helix, 0% strand | Q00403 |
| B | Protein (tata binding protein (tbp)) | protein | 187 | 26% helix, 33% strand | P28147 |
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 675 | 0.65 | 0.75 | 42 | empty |
| 2 | 188 | 0.65 | 0.85 | 30 | empty |
| 3 | 186 | 0.60 | 0.82 | 25 | empty |
| 4 | 108 | 0.54 | 0.84 | 22 | empty |
Interfaces
6 interfaces between chains.
- D–B · 808 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–B · 789 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–D · 737 Ų buried · 83 hydrogen bonds · nucleic-nucleic
- A–B · 666 Ų buried · 8 hydrogen bonds · protein-protein
- D–A · 377 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 1VOL · Tfiib (human core DOMAIN)/TBP (A.THALIANA)/TATA element ternary complex · the same entry in another collection · chain C against C, TM-score 1.00
- P28147 · AlphaFold monomer V2.0 prediction for tata-box-binding protein 1 (P28147) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q00403 · AlphaFold monomer V2.0 prediction for transcription initiation factor iib (Q00403) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q00403
- Every structure of UniProt P28147
- Elsewhere: RCSB PDB 1VOL · PDBe 1VOL · UniProt Q00403 · UniProt P28147
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