Research workbench
1.9 a resolution refined structure of tbp recognizing the minor groove of tataaaag
Analyse 1.9 a resolution refined structure of tbp recognizing the minor groove of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VTO
- Type
- protein + DNA
- Length
- 431 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3'); DNA…
- UniProt
- P28147
- Pockets
- 3 · best druggability 0.33
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3') | dna | 14 | — | — |
| D, F | DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*C)-3') | dna | 14 | — | — |
| A | Tata binding protein | protein | 187 | 25% helix, 34% strand | P28147 |
| B | Tata binding protein | protein | 188 | 26% helix, 34% strand | P28147 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.33 | 0.73 | 13 | empty |
| 2 | 83 | 0.29 | 0.72 | 14 | empty |
| 3 | 50 | 0.28 | 0.75 | 18 | empty |
Interfaces
7 interfaces between chains.
- F–B · 836 Ų buried · 12 hydrogen bonds · protein-nucleic
- D–A · 834 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–A · 830 Ų buried · 7 hydrogen bonds · protein-nucleic
- E–B · 820 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–B · 629 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1VTO · 1.9 a resolution refined structure of tbp recognizing the minor groove of tataaaag · the same entry in another collection · chain B against B, 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 A against A, TM-score 0.99
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 P28147
- Elsewhere: RCSB PDB 1VTO · PDBe 1VTO · UniProt P28147
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