Research workbench
Structure of a. thaliana tbp bound to a DNA site with a C-C mismatch
Analyse Structure of a. thaliana tbp bound to a DNA site with a C-C mismatch in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UEP
- Type
- protein + DNA
- Length
- 434 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tata-box-binding protein 1; DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*CP*GP*GP*GP*CP*A)-3'); DNA…
- UniProt
- P28147
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Tata-box-binding protein 1 | protein | 191 | 25% helix, 35% strand | P28147 |
| E, C | DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*CP*GP*GP*GP*CP*A)-3') | dna | 14 | — | — |
| F, D | DNA (5'-D(*TP*GP*CP*CP*CP*CP*TP*TP*TP*AP*TP*AP*GP*C)-3') | dna | 14 | — | — |
| A | Tata-box-binding protein 1 | protein | 187 | 26% helix, 34% strand | P28147 |
Ligands and binding sites
- FMT · Formic acid · additive · 3 copies · chains B, E, F, C, D
- GOL · Glycerol · additive · 2 copies · chains C, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.73 | 0.77 | 48 | GOL |
| 2 | 56 | 0.61 | 0.93 | 18 | empty |
| 3 | 318 | 0.58 | 0.77 | 29 | empty |
Interfaces
12 interfaces between chains.
- B–E · 815 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–C · 802 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–D · 770 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–F · 763 Ų buried · 8 hydrogen bonds · protein-nucleic
- E–F · 634 Ų buried · 54 hydrogen bonds · nucleic-nucleic
Compared structures
- 6UEP · Structure of A. thaliana TBP bound to a DNA site with a C-C mismatch · the same entry in another collection · chain D against D, 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 6UEP · PDBe 6UEP · UniProt P28147
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