Research workbench
Structure of a. thaliana tbp-ac mismatch DNA site
Analyse Structure of a. thaliana tbp-ac mismatch DNA site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UEO
- Type
- protein + DNA
- Length
- 860 residues
- Chains
- 12
- 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*AP*GP*GP*GP*CP*A)-3'); DNA…
- UniProt
- P28147
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Tata-box-binding protein 1 | protein | 187 | 25% helix, 37% strand | P28147 |
| B, E, H, K | DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3') | dna | 14 | — | — |
| C, F, I, L | DNA (5'-D(*TP*GP*CP*CP*CP*CP*TP*TP*TP*AP*TP*AP*GP*C)-3') | dna | 14 | — | — |
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.76 | 0.79 | 74 | empty |
| 2 | 935 | 0.75 | 0.79 | 58 | empty |
| 3 | 219 | 0.55 | 0.78 | 31 | empty |
| 4 | 222 | 0.52 | 0.77 | 27 | empty |
| 5 | 50 | 0.28 | 0.75 | 9 | empty |
Interfaces
21 interfaces between chains.
- J–L · 839 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–C · 837 Ų buried · 9 hydrogen bonds · protein-nucleic
- J–K · 836 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–E · 834 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–B · 824 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 6UEO · Structure of A. thaliana TBP-AC mismatch DNA site · 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 P28147
- Elsewhere: RCSB PDB 6UEO · PDBe 6UEO · UniProt P28147
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